Variant report

Variant	rs9896940
Chromosome Location	chr17:37895975-37895976
allele	A/G
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	POLR2A	chr17:37893608-37896965	HepG2	liver:	n/a	n/a
2	SIN3AK20	chr17:37895749-37896098	A549	lung:	n/a	n/a
3	MYBL2	chr17:37893721-37896115	HepG2	liver:	n/a	n/a
4	TCF7L2	chr17:37895472-37895983	Hela-S3	cervix:	n/a	n/a
5	MAX	chr17:37895696-37896155	ECC-1	luminal epithelium:	n/a	chr17:37895745-37895755
6	CHD2	chr17:37895806-37895979	HepG2	liver:	n/a	n/a
7	FOXA1	chr17:37895808-37896032	ECC-1	luminal epithelium:	n/a	n/a
8	ZBTB7A	chr17:37895275-37896536	ECC-1	luminal epithelium:	n/a	chr17:37896041-37896052
9	TCF12	chr17:37895221-37896045	HepG2	liver:	n/a	chr17:37895888-37895898
10	FOSL2	chr17:37895530-37896518	A549	lung:	n/a	chr17:37895648-37895659
11	ZEB1	chr17:37895290-37896376	HepG2	liver:	n/a	chr17:37895703-37895710
12	FOS	chr17:37895540-37895983	MCF10A-Er-Src	breast:	n/a	chr17:37895648-37895659
13	MYC	chr17:37895796-37896064	HepG2	liver:	n/a	n/a
14	GATA3	chr17:37895718-37896105	T-47D	breast:	n/a	n/a
15	POLR2A	chr17:37895568-37896202	HepG2	liver:	n/a	n/a
16	ZBTB7A	chr17:37893725-37896638	ECC-1	luminal epithelium:	n/a	chr17:37895048-37895056 chr17:37896041-37896052
17	POLR2A	chr17:37895404-37897262	HCT-116	colon:	n/a	n/a
18	FOXA2	chr17:37895572-37896249	A549	lung:	n/a	n/a
19	TCF12	chr17:37893898-37897334	A549	lung:	n/a	chr17:37896386-37896394 chr17:37897318-37897328 chr17:37895888-37895898 chr17:37897157-37897167
20	POLR2A	chr17:37893572-37897094	HepG2	liver:	n/a	n/a
21	HNF4G	chr17:37895264-37896074	HepG2	liver:	n/a	chr17:37895464-37895479 chr17:37895464-37895479 chr17:37895465-37895478 chr17:37895466-37895478
22	CREB1	chr17:37893479-37897560	HepG2	liver:	n/a	n/a
23	POLR2A	chr17:37895761-37895985	H1-hESC	embryonic stem cell:	n/a	n/a
24	NFIC	chr17:37894917-37896070	HepG2	liver:	n/a	n/a
25	NFIC	chr17:37895616-37896123	ECC-1	luminal epithelium:	n/a	n/a
26	FOXA2	chr17:37895725-37896210	A549	lung:	n/a	n/a
27	MYBL2	chr17:37895193-37896290	HepG2	liver:	n/a	n/a
28	POLR2A	chr17:37894001-37897009	MCF10A-Er-Src	breast:	n/a	n/a
29	TEAD4	chr17:37895224-37896031	HepG2	liver:	n/a	n/a
30	RFX5	chr17:37895527-37896096	HepG2	liver:	n/a	n/a
31	ELF1	chr17:37895773-37896087	K562	blood:	n/a	chr17:37895876-37895888 chr17:37895920-37895933
32	USF1	chr17:37895748-37896014	HepG2	liver:	n/a	chr17:37895881-37895897
33	E2F4	chr17:37895414-37895976	MCF10A-Er-Src	breast:	n/a	chr17:37895747-37895756 chr17:37895781-37895793
34	GATA3	chr17:37895690-37896114	T-47D	breast:	n/a	n/a
35	TCF12	chr17:37895705-37896003	H1-hESC	embryonic stem cell:	n/a	chr17:37895888-37895898
36	TCF12	chr17:37895584-37896206	ECC-1	luminal epithelium:	n/a	chr17:37895888-37895898
37	SIN3AK20	chr17:37895689-37896074	H1-hESC	embryonic stem cell:	n/a	n/a
38	HNF4A	chr17:37895268-37896082	HepG2	liver:	n/a	chr17:37895464-37895479 chr17:37895464-37895479 chr17:37895464-37895479 chr17:37895465-37895478 chr17:37895466-37895478
39	SIN3AK20	chr17:37895688-37896122	HepG2	liver:	n/a	n/a
40	ELF1	chr17:37895261-37896338	HepG2	liver:	n/a	chr17:37895876-37895888 chr17:37895920-37895933
41	FOS	chr17:37895550-37896058	MCF10A-Er-Src	breast:	n/a	chr17:37895648-37895659
42	BCL3	chr17:37895627-37896964	A549	lung:	n/a	chr17:37896200-37896213
43	POLR2A	chr17:37895905-37895997	MCF-7	breast:	n/a	n/a
44	SP1	chr17:37895412-37896209	H1-hESC	embryonic stem cell:	n/a	chr17:37896129-37896143 chr17:37895747-37895756 chr17:37895637-37895647 chr17:37895748-37895757 chr17:37895636-37895648 chr17:37895827-37895841 chr17:37895636-37895648 chr17:37895746-37895758 chr17:37895424-37895436 chr17:37895747-37895757 chr17:37895637-37895646 chr17:37895424-37895436 chr17:37895828-37895841 chr17:37895637-37895647 chr17:37895975-37895988 chr17:37895746-37895758 chr17:37895747-37895757 chr17:37895743-37895757 chr17:37895638-37895647 chr17:37895748-37895757 chr17:37895598-37895612
45	POLR2A	chr17:37893841-37897214	HCT-116	colon:	n/a	n/a
46	FOXA1	chr17:37895286-37896179	HepG2	liver:	n/a	n/a
47	REST	chr17:37895188-37896142	HepG2	liver:	n/a	chr17:37895472-37895490 chr17:37895799-37895812
48	ELF1	chr17:37895409-37896119	HepG2	liver:	n/a	chr17:37895876-37895888 chr17:37895920-37895933
49	MBD4	chr17:37895306-37896828	HepG2	liver:	n/a	n/a
50	FOXA1	chr17:37895636-37896137	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:37884905..37887693-chr17:37894356..37897202,3	MCF-7	breast:
2	chr17:37855582..37857499-chr17:37893190..37897262,3	MCF-7	breast:
3	chr17:37843015..37846318-chr17:37894966..37898626,3	MCF-7	breast:
4	chr17:37806774..37809121-chr17:37895420..37897002,2	MCF-7	breast:
5	chr17:37884020..37887628-chr17:37894260..37898735,4	K562	blood:
6	chr12:118810564..118811520-chr17:37895768..37896672,2	Hela-S3	cervix:
7	chr17:37879887..37888300-chr17:37891591..37897811,12	K562	blood:
8	chr17:37859950..37863403-chr17:37895808..37898808,3	MCF-7	breast:
9	chr17:37820097..37822634-chr17:37895456..37897611,2	K562	blood:
10	chr17:37791351..37794497-chr17:37895466..37898659,4	MCF-7	breast:
11	chr17:37842731..37844399-chr17:37894912..37896553,2	MCF-7	breast:
12	chr11:75110443..75111027-chr17:37895509..37896448,2	Hela-S3	cervix:
13	chr17:37895774..37896647-chr17:62223186..62223748,2	Hela-S3	cervix:
14	chr17:37894865..37896620-chr17:37898811..37901343,2	MCF-7	breast:

Variant related genes	Relation type
GRB7	TF binding region
ENSG00000141738	Chromatin interaction
ENSG00000131748	Chromatin interaction
ENSG00000149273	Chromatin interaction
ENSG00000173991	Chromatin interaction
ENSG00000141736	Chromatin interaction
ENSG00000141741	Chromatin interaction
ENSG00000161395	Chromatin interaction
ENSG00000199753	Chromatin interaction
ENSG00000135090	Chromatin interaction
ENSG00000265178	Chromatin interaction
ENSG00000266402	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs12709364	0.84[AMR][1000 genomes]
rs12937330	1.00[MEX][hapmap]
rs12938117	0.84[AMR][1000 genomes]
rs12938749	0.84[AMR][1000 genomes]
rs12940616	0.84[AMR][1000 genomes]
rs12945253	0.84[AMR][1000 genomes]
rs12946040	0.84[AMR][1000 genomes]
rs12946188	0.84[AMR][1000 genomes]
rs12946792	0.84[AMR][1000 genomes]
rs12947480	0.84[AMR][1000 genomes]
rs12952146	0.84[AMR][1000 genomes]
rs13313573	0.84[AMR][1000 genomes]
rs1453560	1.00[MEX][hapmap]
rs1510475	0.84[AMR][1000 genomes]
rs28392589	0.84[AMR][1000 genomes]
rs28535471	0.84[AMR][1000 genomes]
rs28537796	0.84[AMR][1000 genomes]
rs28580691	0.84[AMR][1000 genomes]
rs28621669	0.84[AMR][1000 genomes]
rs28648398	0.84[AMR][1000 genomes]
rs28661421	0.84[AMR][1000 genomes]
rs28695941	0.84[AMR][1000 genomes]
rs28723017	0.84[AMR][1000 genomes]
rs28880017	0.84[AMR][1000 genomes]
rs28896477	0.84[AMR][1000 genomes]
rs34053394	0.84[AMR][1000 genomes]
rs34291217	0.84[AMR][1000 genomes]
rs34485135	0.84[AMR][1000 genomes]
rs34518282	0.84[AMR][1000 genomes]
rs34640000	0.84[AMR][1000 genomes]
rs34654193	0.84[AMR][1000 genomes]
rs34925681	0.84[AMR][1000 genomes]
rs35088469	0.84[AMR][1000 genomes]
rs35105110	0.84[AMR][1000 genomes]
rs35352075	0.84[AMR][1000 genomes]
rs35405174	0.84[AMR][1000 genomes]
rs35506518	0.84[AMR][1000 genomes]
rs35770042	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35938199	0.84[AMR][1000 genomes]
rs4252665	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4622539	0.84[AMR][1000 genomes]
rs58075375	0.84[AMR][1000 genomes]
rs66763967	0.84[AMR][1000 genomes]
rs67605703	0.84[AMR][1000 genomes]
rs71369791	0.84[AMR][1000 genomes]
rs71369792	0.84[AMR][1000 genomes]
rs73302152	0.84[AMR][1000 genomes]
rs73304123	0.84[AMR][1000 genomes]
rs7503018	1.00[MEX][hapmap]
rs8068125	0.84[AMR][1000 genomes]
rs8069893	0.84[AMR][1000 genomes]
rs8076347	1.00[MEX][hapmap]
rs8079075	1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs9652840	1.00[CEU][hapmap]
rs9891131	1.00[CEU][hapmap];1.00[MEX][hapmap];0.91[EUR][1000 genomes]
rs9894898	0.84[AMR][1000 genomes]
rs9898031	0.84[AMR][1000 genomes]
rs9900019	0.84[AMR][1000 genomes]
rs9900538	0.84[AMR][1000 genomes]
rs9901483	1.00[MEX][hapmap]
rs9901617	0.84[AMR][1000 genomes]
rs9901917	0.84[AMR][1000 genomes]
rs9902621	0.84[AMR][1000 genomes]
rs9904277	0.84[AMR][1000 genomes]
rs9904834	0.84[AMR][1000 genomes]
rs9907096	0.84[AMR][1000 genomes]
rs9907564	0.84[AMR][1000 genomes]
rs9907794	0.84[AMR][1000 genomes]
rs9907966	1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs9908694	1.00[MEX][hapmap]
rs9908983	0.84[AMR][1000 genomes]
rs9910678	1.00[CEU][hapmap];1.00[MEX][hapmap];0.91[EUR][1000 genomes]
rs9911069	0.84[AMR][1000 genomes]
rs9911669	0.84[AMR][1000 genomes]
rs9911688	1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs9912095	0.84[AMR][1000 genomes]
rs9913596	0.84[AMR][1000 genomes]
rs9913769	1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs9913957	1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs9914302	0.84[AMR][1000 genomes]
rs9914665	0.84[AMR][1000 genomes]
rs9915509	0.84[AMR][1000 genomes]
rs9916259	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1056234	chr17:37862605-37909988	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv908219	chr17:37880265-37917633	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37893600-37896000	Active TSS	Liver	Liver
2	chr17:37893600-37897000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr17:37893600-37897200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr17:37893600-37897200	Active TSS	Esophagus	oesophagus
5	chr17:37893800-37896000	Bivalent Enhancer	Fetal Brain Male	brain
6	chr17:37893800-37896200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr17:37893800-37896200	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr17:37893800-37896200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
9	chr17:37893800-37896400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr17:37893800-37896400	Bivalent/Poised TSS	HepG2	liver
11	chr17:37893800-37897200	Active TSS	Fetal Kidney	kidney
12	chr17:37893800-37897200	Active TSS	Gastric	stomach
13	chr17:37893800-37897400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr17:37893800-37897600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr17:37894000-37896000	Active TSS	Right Atrium	heart
16	chr17:37894000-37896000	Active TSS	A549	lung
17	chr17:37894000-37896000	Active TSS	Hela-S3	cervix
18	chr17:37894000-37896200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr17:37894000-37896400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr17:37894000-37896400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr17:37894000-37896400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
22	chr17:37894000-37896400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
23	chr17:37894000-37896600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr17:37894000-37896600	Active TSS	Pancreas	Pancrea
25	chr17:37894000-37896800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr17:37894200-37896400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr17:37894200-37896400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
28	chr17:37894200-37896800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr17:37894400-37896000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr17:37894400-37896000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
31	chr17:37894400-37896200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
32	chr17:37894400-37896200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr17:37894400-37896400	Bivalent/Poised TSS	Stomach Mucosa	stomach
34	chr17:37894600-37896000	Active TSS	Rectal Smooth Muscle	rectum
35	chr17:37894600-37896400	Bivalent Enhancer	Brain Germinal Matrix	brain
36	chr17:37894800-37896000	Flanking Bivalent TSS/Enh	Thymus	Thymus
37	chr17:37894800-37897400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:37894800-37897600	Enhancers	Left Ventricle	heart
39	chr17:37895000-37896000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr17:37895000-37896000	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr17:37895000-37896000	Bivalent Enhancer	Fetal Brain Female	brain
42	chr17:37895000-37896000	Active TSS	Placenta Amnion	Placenta Amnion
43	chr17:37895000-37896400	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr17:37895000-37896600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr17:37895200-37896000	Active TSS	Duodenum Mucosa	Duodenum
46	chr17:37895200-37896200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr17:37895200-37896400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
48	chr17:37895200-37896400	Bivalent Enhancer	Brain Anterior Caudate	brain
49	chr17:37895200-37896400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
50	chr17:37895200-37896400	Enhancers	GM12878-XiMat	blood

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