Variant report

Variant	rs11589952
Chromosome Location	chr1:169453209-169453210
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:58)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:58 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CCNT2	chr1:169452763-169453712	K562	blood:	n/a	n/a
2	MAZ	chr1:169452799-169453215	K562	blood:	n/a	n/a
3	RFX5	chr1:169452660-169453550	Hela-S3	cervix:	n/a	chr1:169452824-169452833
4	MAX	chr1:169452762-169453263	MCF-7	breast:	n/a	n/a
5	FOXA1	chr1:169452644-169453231	HepG2	liver:	n/a	n/a
6	ARID3A	chr1:169452806-169453335	K562	blood:	n/a	n/a
7	MAX	chr1:169452753-169453623	Hela-S3	cervix:	n/a	n/a
8	USF1	chr1:169452613-169453275	K562	blood:	n/a	n/a
9	MXI1	chr1:169452691-169453459	HepG2	liver:	n/a	n/a
10	MXI1	chr1:169452742-169453593	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:169452374-169456758	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr1:169452668-169456351	Hela-S3	cervix:	n/a	n/a
13	EP300	chr1:169452368-169453399	K562	blood:	n/a	chr1:169452398-169452412
14	MAFF	chr1:169452704-169453211	HepG2	liver:	n/a	n/a
15	CUX1	chr1:169452815-169453536	K562	blood:	n/a	n/a
16	MYC	chr1:169452672-169453483	K562	blood:	n/a	n/a
17	USF2	chr1:169452737-169453452	Hela-S3	cervix:	n/a	chr1:169452942-169452953
18	POLR2A	chr1:169452665-169453713	HepG2	liver:	n/a	n/a
19	POLR2A	chr1:169452788-169453546	HepG2	liver:	n/a	n/a
20	CHD2	chr1:169453025-169453724	K562	blood:	n/a	n/a
21	SIN3AK20	chr1:169452809-169453225	K562	blood:	n/a	n/a
22	MAX	chr1:169452679-169453253	K562	blood:	n/a	n/a
23	MYC	chr1:169452634-169454733	MCF10A-Er-Src	breast:	n/a	n/a
24	TBL1XR1	chr1:169452606-169453618	K562	blood:	n/a	n/a
25	FOS	chr1:169452844-169453743	MCF10A-Er-Src	breast:	n/a	chr1:169452868-169452880
26	SIN3AK20	chr1:169452581-169456049	MCF-7	breast:	n/a	n/a
27	JUND	chr1:169452750-169453715	K562	blood:	n/a	chr1:169452868-169452880
28	POLR2A	chr1:169451934-169453706	K562	blood:	n/a	n/a
29	POLR2A	chr1:169452556-169453875	H1-hESC	embryonic stem cell:	n/a	n/a
30	MYC	chr1:169452677-169453536	K562	blood:	n/a	n/a
31	MYBL2	chr1:169452674-169453270	HepG2	liver:	n/a	n/a
32	MAX	chr1:169452777-169453229	Hela-S3	cervix:	n/a	n/a
33	KAP1	chr1:169452757-169453593	U2OS	brain:	n/a	n/a
34	MAX	chr1:169452796-169453223	NB4	blood:	n/a	n/a
35	E2F4	chr1:169452857-169453848	MCF10A-Er-Src	breast:	n/a	chr1:169453020-169453027
36	MAX	chr1:169452726-169453215	K562	blood:	n/a	n/a
37	CBX3	chr1:169452686-169453680	K562	blood:	n/a	n/a
38	FOS	chr1:169452813-169453647	MCF10A-Er-Src	breast:	n/a	chr1:169452868-169452880
39	SETDB1	chr1:169452761-169453223	U2OS	brain:	n/a	n/a
40	IRF1	chr1:169452770-169453213	K562	blood:	n/a	chr1:169453059-169453066
41	STAT3	chr1:169452857-169453801	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr1:169452526-169456603	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr1:169451926-169456727	IMR90	lung:	n/a	n/a
44	MAX	chr1:169452723-169453525	K562	blood:	n/a	n/a
45	HCFC1	chr1:169452490-169456441	Hela-S3	cervix:	n/a	n/a
46	CREB1	chr1:169452648-169453312	HepG2	liver:	n/a	n/a
47	STAT3	chr1:169452866-169453779	MCF10A-Er-Src	breast:	n/a	n/a
48	CHD1	chr1:169452645-169456936	IMR90	lung:	n/a	chr1:169453020-169453027 chr1:169455009-169455019 chr1:169454476-169454486
49	ZC3H11A	chr1:169452663-169453225	K562	blood:	n/a	n/a
50	HEY1	chr1:169452737-169453239	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:169451858..169456935-chr1:169476541..169486862,15	MCF-7	breast:
2	chr1:169428536..169430863-chr1:169451257..169453654,2	K562	blood:
3	chr1:169337822..169339719-chr1:169451874..169454199,3	K562	blood:
4	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
5	chr1:169338121..169342264-chr1:169451874..169455112,4	K562	blood:
6	chr1:169437031..169439523-chr1:169451162..169453352,3	MCF-7	breast:
7	chr1:169452217..169454597-chr1:169772651..169775174,2	K562	blood:
8	chr1:169434019..169436756-chr1:169452207..169454585,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213062	TF binding region
ENSG00000198734	Chromatin interaction
ENSG00000117477	Chromatin interaction
ENSG00000234437	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10919175	0.80[YRI][hapmap]
rs17518601	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs17518769	1.00[CEU][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17577986	1.00[CEU][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59849608	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169430000-169453400	Weak transcription	Colonic Mucosa	Colon
2	chr1:169430000-169453800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:169430000-169454000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:169430000-169454400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:169430000-169454400	Weak transcription	Spleen	Spleen
6	chr1:169444200-169454000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:169446800-169454200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:169446800-169454200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:169448000-169457000	Active TSS	Right Ventricle	heart
10	chr1:169449000-169453600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:169450000-169456000	Active TSS	Psoas Muscle	Psoas
12	chr1:169451000-169453800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:169451000-169454000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:169451600-169453600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:169451600-169457000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:169451800-169453800	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr1:169451800-169455400	Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr1:169452000-169453400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr1:169452000-169453400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr1:169452000-169453800	Enhancers	Primary hematopoietic stem cells	blood
21	chr1:169452000-169453800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr1:169452000-169454200	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr1:169452200-169453400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:169452200-169453600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr1:169452200-169453800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr1:169452200-169456200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:169452400-169454200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:169452400-169454200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr1:169452400-169454200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr1:169452400-169454400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:169452400-169454800	Active TSS	Right Atrium	heart
32	chr1:169452600-169453400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:169452600-169453400	Enhancers	Primary T cells from cord blood	blood
34	chr1:169452600-169453800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr1:169452600-169453800	Enhancers	Fetal Muscle Leg	muscle
36	chr1:169452600-169453800	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr1:169452600-169453800	Flanking Active TSS	HSMM	muscle
38	chr1:169452600-169454000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr1:169452600-169454000	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr1:169452600-169454000	Enhancers	HUVEC	blood vessel
41	chr1:169452600-169454200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:169452600-169454200	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr1:169452600-169454200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:169452600-169454200	Flanking Active TSS	Hela-S3	cervix
45	chr1:169452600-169454400	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr1:169452600-169454400	Flanking Active TSS	Fetal Intestine Small	intestine
47	chr1:169452600-169454600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:169452600-169454600	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr1:169452600-169454600	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr1:169452600-169454800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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