Variant report

Variant	rs2429458
Chromosome Location	chr11:63992706-63992707
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:71)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:71 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr11:63992639-63993031	HL-60	blood:	n/a	n/a
2	POLR2A	chr11:63992607-63993204	GM12891	blood:	n/a	n/a
3	POLR2A	chr11:63989232-63995299	K562	blood:	n/a	n/a
4	HCFC1	chr11:63992684-63994367	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr11:63989880-63995323	GM12891	blood:	n/a	n/a
6	POLR2A	chr11:63991338-63994677	GM12891	blood:	n/a	n/a
7	POLR2A	chr11:63991343-63995010	U87	brain:	n/a	n/a
8	MTA3	chr11:63991287-63995175	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:63991349-63994680	GM12891	blood:	n/a	n/a
10	POLR2A	chr11:63991516-63995277	Raji	blood:	n/a	n/a
11	POLR2A	chr11:63991337-63995010	U87	brain:	n/a	n/a
12	POLR2A	chr11:63991399-63994678	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:63990418-63994603	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:63989946-63994682	HL-60	blood:	n/a	n/a
15	POLR2A	chr11:63991751-63993094	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr11:63992564-63994729	HepG2	liver:	n/a	chr11:63993229-63993239 chr11:63993079-63993088
17	MAZ	chr11:63992605-63994798	IMR90	lung:	n/a	chr11:63993229-63993239 chr11:63993079-63993088
18	POLR2A	chr11:63990068-63995245	GM18505	blood:	n/a	n/a
19	POLR2A	chr11:63992302-63993190	GM12878	blood:	n/a	n/a
20	POLR2A	chr11:63989981-63995376	GM12892	blood:	n/a	n/a
21	MTA3	chr11:63992314-63992870	GM12878	blood:	n/a	n/a
22	POLR2A	chr11:63991347-63994715	GM12892	blood:	n/a	n/a
23	SPI1	chr11:63992376-63993016	HL-60	blood:	n/a	n/a
24	POLR2A	chr11:63992383-63994299	MCF-7	breast:	n/a	n/a
25	POLR2A	chr11:63989888-63995214	K562	blood:	n/a	n/a
26	CHD2	chr11:63992660-63994075	K562	blood:	n/a	n/a
27	BCL3	chr11:63992133-63992794	GM12878	blood:	n/a	n/a
28	SMARCB1	chr11:63992635-63994640	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr11:63990059-63994553	K562	blood:	n/a	n/a
30	POLR2A	chr11:63989881-63994799	GM12878	blood:	n/a	n/a
31	POLR2A	chr11:63990003-63994887	K562	blood:	n/a	n/a
32	POLR2A	chr11:63991329-63994676	HUVEC	blood vessel:	n/a	n/a
33	HEY1	chr11:63992678-63992963	K562	blood:	n/a	n/a
34	POLR2A	chr11:63992694-63992733	MCF-7	breast:	n/a	n/a
35	POLR2A	chr11:63990960-63994308	GM12892	blood:	n/a	n/a
36	POLR2A	chr11:63990076-63994151	K562	blood:	n/a	n/a
37	STAT5A	chr11:63991772-63994864	GM12878	blood:	n/a	chr11:63993231-63993243 chr11:63993237-63993249
38	POLR2A	chr11:63990163-63994910	GM12878	blood:	n/a	n/a
39	POLR2A	chr11:63989900-63994663	GM12892	blood:	n/a	n/a
40	POLR2A	chr11:63991181-63994492	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr11:63989222-63995360	K562	blood:	n/a	n/a
42	POLR2A	chr11:63992613-63992976	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr11:63991404-63994814	GM12878	blood:	n/a	n/a
44	POLR2A	chr11:63992581-63995191	HepG2	liver:	n/a	n/a
45	POLR2A	chr11:63990053-63994681	GM18951	blood:	n/a	n/a
46	YY1	chr11:63992670-63992994	K562	blood:	n/a	n/a
47	POLR2A	chr11:63989892-63994921	GM12878	blood:	n/a	n/a
48	POLR2A	chr11:63991528-63994560	NB4	blood:	n/a	n/a
49	POLR2A	chr11:63991464-63994691	PBDE	blood:	n/a	n/a
50	POLR2A	chr11:63990003-63995334	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:63991030..63993449-chr16:4673277..4676059,2	K562	blood:
2	chr11:63992038..63994216-chr11:64062874..64065506,2	MCF-7	breast:
3	chr11:63990938..63995618-chr11:64068467..64075569,11	MCF-7	breast:
4	chr1:113932898..113933685-chr11:63992576..63993445,2	Hela-S3	cervix:
5	chr11:63962580..63965391-chr11:63991959..63994483,2	MCF-7	breast:
6	chr11:63991810..63993878-chr11:64081220..64083594,2	K562	blood:
7	chr11:63992108..63994970-chr11:64050201..64053443,5	MCF-7	breast:
8	chr11:63951654..63956341-chr11:63991514..63996131,9	MCF-7	breast:

No data

Variant related genes	Relation type
TRPT1	TF binding region
NUDT22	TF binding region
ENSG00000173153	Chromatin interaction
ENSG00000182450	Chromatin interaction
ENSG00000002330	Chromatin interaction
ENSG00000081026	Chromatin interaction
ENSG00000219435	Chromatin interaction
ENSG00000173264	Chromatin interaction
ENSG00000168439	Chromatin interaction
ENSG00000207024	Chromatin interaction
ENSG00000102858	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs654573	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs655896	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
2	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
3	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
4	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
5	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
6	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
7	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
8	nsv897662	chr11:63889749-64150370	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
9	nsv897664	chr11:63919742-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
10	nsv468592	chr11:63924446-64042997	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
11	nsv555184	chr11:63924446-64042997	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
12	nsv897665	chr11:63927695-64026144	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	155 gene(s)	inside rSNPs	diseases
13	nsv897666	chr11:63929493-64026144	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	155 gene(s)	inside rSNPs	diseases
14	nsv869944	chr11:63932152-64123062	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
15	nsv468593	chr11:63941734-64089874	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
16	nsv555185	chr11:63941734-64089874	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
17	nsv555186	chr11:63949095-64097233	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
18	nsv468595	chr11:63953121-64027888	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases
19	nsv555187	chr11:63953121-64027888	Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases
20	nsv897667	chr11:63964657-64078380	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
21	nsv897668	chr11:63964657-64085298	Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	163 gene(s)	inside rSNPs	diseases
22	nsv897669	chr11:63964657-64089874	Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
23	nsv897670	chr11:63964657-64097233	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
24	nsv897671	chr11:63964657-64150370	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
25	nsv541061	chr11:63970174-64010995	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
26	nsv832186	chr11:63972260-64170059	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	180 gene(s)	inside rSNPs	diseases
27	nsv897672	chr11:63979643-64082807	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
28	esv1802320	chr11:63987425-64154633	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
29	nsv897673	chr11:63991581-64018687	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
30	esv992196	chr11:63992534-64002355	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2429458	SYPL2	trans	lymphoblastoid	seeQTL
rs2429458	TRPT1	cis	lymphoblastoid	seeQTL
rs2429458	PPP1R14B	cis	lymphoblastoid	seeQTL
rs2429458	ENTHD1	trans	lymphoblastoid	seeQTL
rs2429458	SHE	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63971600-63992800	Weak transcription	Fetal Kidney	kidney
2	chr11:63973600-63993000	Weak transcription	Aorta	Aorta
3	chr11:63975600-63992800	Weak transcription	Fetal Lung	lung
4	chr11:63975800-63993000	Weak transcription	Small Intestine	intestine
5	chr11:63976400-63992800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:63976800-63992800	Weak transcription	Brain Substantia Nigra	brain
7	chr11:63988600-63992800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:63988800-63992800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr11:63988800-63992800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:63988800-63993000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:63990000-63993000	Genic enhancers	Spleen	Spleen
12	chr11:63990200-63993000	Enhancers	Stomach Mucosa	stomach
13	chr11:63990400-63992800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:63991000-63992800	Enhancers	HMEC	breast
15	chr11:63991000-63993000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:63991400-63992800	Enhancers	A549	lung
17	chr11:63991400-63992800	Enhancers	NH-A	brain
18	chr11:63991400-63992800	Enhancers	NHDF-Ad	bronchial
19	chr11:63991400-63993000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:63991600-63992800	Enhancers	Hela-S3	cervix
21	chr11:63991800-63992800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr11:63991800-63992800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:63991800-63992800	Genic enhancers	Right Ventricle	heart
24	chr11:63991800-63993000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr11:63991800-63993000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
26	chr11:63992000-63992800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr11:63992000-63992800	Enhancers	Primary T cells fromperipheralblood	blood
28	chr11:63992000-63992800	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr11:63992000-63992800	Enhancers	Pancreas	Pancrea
30	chr11:63992000-63992800	Enhancers	HSMMtube	muscle
31	chr11:63992000-63992800	Enhancers	NHEK	skin
32	chr11:63992000-63993000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr11:63992000-63993000	Enhancers	Primary B cells from cord blood	blood
34	chr11:63992000-63993200	Enhancers	Fetal Heart	heart
35	chr11:63992200-63992800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr11:63992200-63992800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
37	chr11:63992200-63992800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr11:63992200-63992800	Enhancers	Brain Hippocampus Middle	brain
39	chr11:63992200-63992800	Enhancers	Esophagus	oesophagus
40	chr11:63992200-63992800	Enhancers	Fetal Intestine Large	intestine
41	chr11:63992200-63992800	Enhancers	Fetal Thymus	thymus
42	chr11:63992200-63992800	Enhancers	Psoas Muscle	Psoas
43	chr11:63992200-63993000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr11:63992200-63993000	Enhancers	Primary B cells from peripheral blood	blood
45	chr11:63992200-63993000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr11:63992200-63993000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr11:63992200-63993000	Enhancers	Placenta	Placenta
48	chr11:63992200-63993000	Enhancers	Right Atrium	heart
49	chr11:63992200-63993200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
50	chr11:63992400-63992800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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