Variant report

Variant	rs3759057
Chromosome Location	chr11:64125680-64125681
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr11:64124546-64127782	Hela-S3	cervix:	n/a	n/a
2	TBL1XR1	chr11:64125482-64125682	K562	blood:	n/a	n/a
3	SMARCB1	chr11:64125210-64127144	Hela-S3	cervix:	n/a	n/a
4	YY1	chr11:64125428-64125874	K562	blood:	n/a	n/a
5	BHLHE40	chr11:64125554-64126887	HepG2	liver:	n/a	chr11:64126316-64126332 chr11:64126780-64126796 chr11:64126632-64126648 chr11:64126633-64126649
6	TCF7L2	chr11:64125416-64125799	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr11:64125476-64125683	A549	lung:	n/a	n/a
8	UBTF	chr11:64125490-64125756	K562	blood:	n/a	n/a
9	MAX	chr11:64125485-64127208	HepG2	liver:	n/a	chr11:64125961-64125977 chr11:64125970-64125977 chr11:64125969-64125978 chr11:64125972-64125988 chr11:64125725-64125735
10	POLR2A	chr11:64125316-64127393	Hela-S3	cervix:	n/a	n/a
11	GTF2F1	chr11:64125400-64125922	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr11:64125314-64126017	K562	blood:	n/a	n/a
13	BRCA1	chr11:64125398-64125705	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr11:64125414-64126909	GM12878	blood:	n/a	n/a
15	POLR2A	chr11:64125303-64127100	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr11:64125628-64125761	HepG2	liver:	n/a	n/a
17	YY1	chr11:64125377-64125889	K562	blood:	n/a	chr11:64125871-64125885
18	POLR2A	chr11:64125026-64127534	K562	blood:	n/a	n/a
19	POLR2A	chr11:64125487-64126143	GM12892	blood:	n/a	n/a
20	MAX	chr11:64125298-64127158	K562	blood:	n/a	chr11:64125961-64125977 chr11:64125970-64125977 chr11:64125969-64125978 chr11:64125972-64125988 chr11:64125725-64125735
21	MAX	chr11:64125460-64126256	A549	lung:	n/a	chr11:64125961-64125977 chr11:64125970-64125977 chr11:64125969-64125978 chr11:64125972-64125988 chr11:64125725-64125735
22	ZBTB7A	chr11:64125637-64125766	HepG2	liver:	n/a	n/a
23	SMARCC2	chr11:64124862-64126548	Hela-S3	cervix:	n/a	n/a
24	BHLHE40	chr11:64125430-64126924	K562	blood:	n/a	chr11:64126316-64126332 chr11:64126780-64126796 chr11:64126632-64126648 chr11:64126633-64126649
25	ELF1	chr11:64125424-64125913	K562	blood:	n/a	chr11:64125733-64125745
26	MAFK	chr11:64125403-64126052	Hela-S3	cervix:	n/a	n/a
27	NR2F2	chr11:64125226-64126455	K562	blood:	n/a	n/a
28	POLR2A	chr11:64125447-64125738	GM12878	blood:	n/a	n/a
29	MXI1	chr11:64125646-64127658	SK-N-SH	brain:	n/a	n/a
30	ZBTB7A	chr11:64125127-64127287	K562	blood:	n/a	n/a
31	POLR2A	chr11:64125206-64126100	K562	blood:	n/a	n/a
32	POLR2A	chr11:64125340-64125736	K562	blood:	n/a	n/a
33	CCNT2	chr11:64125401-64125982	K562	blood:	n/a	n/a
34	POLR2A	chr11:64125379-64125946	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr11:64125607-64125727	ProgFib	skin:	n/a	n/a
36	JUND	chr11:64125332-64125742	K562	blood:	n/a	chr11:64125503-64125511
37	POLR2A	chr11:64125374-64125818	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr11:64125281-64125859	HCT-116	colon:	n/a	n/a
39	GABPA	chr11:64125429-64125861	K562	blood:	n/a	n/a
40	POLR2A	chr11:64125202-64125810	HCT-116	colon:	n/a	n/a
41	CBX3	chr11:64125256-64126131	K562	blood:	n/a	n/a
42	EP300	chr11:64125389-64125694	K562	blood:	n/a	n/a
43	ZBTB7A	chr11:64125386-64127369	ECC-1	luminal epithelium:	n/a	n/a
44	MAX	chr11:64125381-64125903	K562	blood:	n/a	chr11:64125725-64125735
45	MAZ	chr11:64124649-64125918	IMR90	lung:	n/a	chr11:64125278-64125288 chr11:64125274-64125284 chr11:64125725-64125735
46	HEY1	chr11:64125513-64125753	K562	blood:	n/a	n/a
47	MAZ	chr11:64125259-64127214	Hela-S3	cervix:	n/a	chr11:64125961-64125977 chr11:64125278-64125288 chr11:64125970-64125977 chr11:64125969-64125978 chr11:64125972-64125988 chr11:64125274-64125284 chr11:64125725-64125735
48	TAF1	chr11:64125394-64125749	Hela-S3	cervix:	n/a	n/a
49	MAX	chr11:64125327-64127627	A549	lung:	n/a	chr11:64125961-64125977 chr11:64125970-64125977 chr11:64125969-64125978 chr11:64125972-64125988 chr11:64127233-64127243 chr11:64125725-64125735
50	SMARCC1	chr11:64125052-64126564	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:64110456..64113002-chr11:64125236..64127679,2	MCF-7	breast:
2	chr11:63972047..63977847-chr11:64122012..64128099,8	K562	blood:
3	chr11:64041009..64043331-chr11:64125161..64128159,2	MCF-7	breast:
4	chr11:64082853..64088243-chr11:64119014..64129028,17	MCF-7	breast:
5	chr11:64070250..64072559-chr11:64125217..64126731,2	MCF-7	breast:
6	chr11:64125330..64128537-chr11:64215213..64218115,3	MCF-7	breast:
7	chr11:64073021..64075424-chr11:64122972..64125774,2	MCF-7	breast:
8	chr11:64017685..64020898-chr11:64124130..64127721,3	MCF-7	breast:
9	chr11:64000008..64002901-chr11:64125113..64127418,2	MCF-7	breast:
10	chr11:64070986..64076286-chr11:64124810..64128616,7	K562	blood:
11	chr11:64119430..64124364-chr11:64124831..64128743,7	MCF-7	breast:
12	chr11:64013360..64015283-chr11:64125680..64128243,2	MCF-7	breast:
13	chr11:64004012..64005762-chr11:64124323..64126720,2	MCF-7	breast:
14	chr11:64062668..64065011-chr11:64124225..64126837,3	MCF-7	breast:
15	chr11:64124497..64126994-chr11:64509396..64512374,2	K562	blood:
16	chr11:64008386..64010951-chr11:64125361..64127756,4	MCF-7	breast:
17	chr11:64053151..64055063-chr11:64124109..64127002,2	K562	blood:
18	chr11:64083913..64086967-chr11:64122125..64127376,8	MCF-7	breast:
19	chr11:64125259..64126829-chr11:64127521..64129918,2	MCF-7	breast:
20	chr11:64080620..64083894-chr11:64124180..64128334,3	MCF-7	breast:
21	chr11:64124989..64126699-chr11:64216058..64218143,2	K562	blood:
22	chr11:64124540..64126165-chr11:64416805..64418709,2	MCF-7	breast:
23	chr11:63972384..63977847-chr11:64121311..64126015,8	K562	blood:

Variant related genes	Relation type
RPS6KA4	TF binding region
ENSG00000068831	Chromatin interaction
ENSG00000173113	Chromatin interaction
ENSG00000173486	Chromatin interaction
ENSG00000168071	Chromatin interaction
ENSG00000207024	Chromatin interaction
ENSG00000110011	Chromatin interaction
ENSG00000256116	Chromatin interaction
ENSG00000181908	Chromatin interaction
ENSG00000149781	Chromatin interaction
ENSG00000173153	Chromatin interaction
ENSG00000126432	Chromatin interaction
ENSG00000182450	Chromatin interaction
ENSG00000256940	Chromatin interaction
ENSG00000173511	Chromatin interaction
ENSG00000162302	Chromatin interaction
ENSG00000149782	Chromatin interaction
ENSG00000173457	Chromatin interaction
ENSG00000219435	Chromatin interaction
ENSG00000173264	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs61886887	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61886888	0.92[EUR][1000 genomes]
rs61886927	0.86[EUR][1000 genomes]
rs61886930	1.00[AFR][1000 genomes]
rs660442	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
6	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
7	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
8	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
9	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
10	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
11	nsv897679	chr11:63994692-64150370	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
12	nsv897682	chr11:63999529-64170500	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
13	nsv1043277	chr11:64002997-64132030	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
14	nsv897685	chr11:64048912-64150370	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
15	nsv818841	chr11:64097233-64129722	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
16	nsv897688	chr11:64107735-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
17	nsv897689	chr11:64109118-64148420	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
18	nsv897690	chr11:64118422-64135298	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
19	nsv897691	chr11:64118422-64137875	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
20	nsv832187	chr11:64121969-64312300	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' 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	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3759057	AP003774.1	cis	Whole Blood	GTEx
rs3759057	CCDC88B	cis	Esophagus Mucosa	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64121800-64126000	Enhancers	Placenta	Placenta
2	chr11:64122000-64126000	Enhancers	Fetal Muscle Trunk	muscle
3	chr11:64123000-64125800	Weak transcription	Fetal Brain Male	brain
4	chr11:64123000-64126000	Weak transcription	Psoas Muscle	Psoas
5	chr11:64123200-64125800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr11:64123200-64125800	Weak transcription	Brain Angular Gyrus	brain
7	chr11:64123200-64126000	Weak transcription	Aorta	Aorta
8	chr11:64123200-64126000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr11:64123200-64126000	Enhancers	HMEC	breast
10	chr11:64123200-64126200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr11:64123400-64125800	Enhancers	Stomach Mucosa	stomach
12	chr11:64123400-64126000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:64123800-64125800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:64123800-64126200	Enhancers	Pancreas	Pancrea
15	chr11:64124000-64125800	Enhancers	Fetal Intestine Small	intestine
16	chr11:64124000-64126000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr11:64124000-64126200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:64124200-64125800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:64124200-64125800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:64124200-64125800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:64124200-64126000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr11:64124200-64126000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr11:64124200-64126000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:64124200-64126000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:64124200-64126000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr11:64124200-64126200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr11:64124200-64126200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr11:64124200-64126200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr11:64124200-64126400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr11:64124400-64125800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:64124400-64125800	Flanking Active TSS	HepG2	liver
32	chr11:64124400-64126000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:64124400-64126000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:64124400-64126200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr11:64124600-64125800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr11:64124600-64125800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr11:64124600-64125800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr11:64124600-64125800	Enhancers	Fetal Intestine Large	intestine
39	chr11:64124600-64126000	Enhancers	Primary T cells fromperipheralblood	blood
40	chr11:64124600-64126000	Enhancers	Fetal Muscle Leg	muscle
41	chr11:64124800-64125800	Enhancers	Primary T cells from cord blood	blood
42	chr11:64124800-64126000	Enhancers	Fetal Thymus	thymus
43	chr11:64124800-64126600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:64125000-64125800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr11:64125000-64125800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:64125000-64125800	Enhancers	Adipose Nuclei	Adipose
47	chr11:64125000-64125800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr11:64125000-64126000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr11:64125000-64126000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:64125000-64126000	Enhancers	Esophagus	oesophagus

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