Variant report

Variant	rs4718988
Chromosome Location	chr7:70194024-70194025
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	chr7:70193682-70194755	GM12878	blood:	n/a	n/a
2	MTA3	chr7:70193760-70194670	GM12878	blood:	n/a	n/a
3	EBF1	chr7:70193712-70194140	GM12878	blood:	n/a	n/a
4	BHLHE40	chr7:70193857-70194815	GM12878	blood:	n/a	n/a
5	TBP	chr7:70193833-70194116	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr7:70193766-70194369	GM12878	blood:	n/a	chr7:70194297-70194308
7	NFIC	chr7:70193675-70194873	GM12878	blood:	n/a	chr7:70194584-70194601
8	YY1	chr7:70193931-70194277	GM12892	blood:	n/a	n/a
9	CTCF	chr7:70193920-70194070	HEEpiC	esophagus:	n/a	n/a
10	YY1	chr7:70193859-70194384	GM12878	blood:	n/a	chr7:70194297-70194308
11	CHD2	chr7:70193835-70194085	GM12878	blood:	n/a	n/a
12	TBP	chr7:70193851-70194896	GM12878	blood:	n/a	n/a
13	ZNF384	chr7:70193679-70194232	GM12878	blood:	n/a	n/a
14	POLR2A	chr7:70193651-70194343	H1-hESC	embryonic stem cell:	n/a	n/a
15	ELF1	chr7:70193895-70194411	GM12878	blood:	n/a	n/a
16	MAZ	chr7:70193878-70194054	GM12878	blood:	n/a	n/a
17	CTBP2	chr7:70193894-70194317	H1-hESC	embryonic stem cell:	n/a	n/a
18	TBL1XR1	chr7:70193811-70194617	GM12878	blood:	n/a	n/a
19	BCL11A	chr7:70193763-70194026	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr7:70193846-70194094	H1-hESC	embryonic stem cell:	n/a	n/a
21	ZNF263	chr7:70193755-70194129	HEK293-T-REx	kidney:	n/a	chr7:70194022-70194031 chr7:70193864-70193885
22	ZNF143	chr7:70193973-70194628	GM12878	blood:	n/a	n/a
23	STAT5A	chr7:70193980-70194745	GM12878	blood:	n/a	chr7:70194391-70194402 chr7:70194033-70194044 chr7:70194409-70194418 chr7:70194256-70194268 chr7:70194410-70194419
24	MAX	chr7:70193847-70194167	GM12878	blood:	n/a	n/a
25	POLR2A	chr7:70193962-70194215	H1-hESC	embryonic stem cell:	n/a	n/a
26	KAP1	chr7:70193721-70194246	HEK293	kidney:	n/a	n/a
27	MTA3	chr7:70193650-70194919	GM12878	blood:	n/a	n/a
28	PML	chr7:70193606-70194806	GM12878	blood:	n/a	n/a
29	POLR2A	chr7:70194019-70194027	GM12878	blood:	n/a	n/a
30	RCOR1	chr7:70193951-70194598	GM12878	blood:	n/a	n/a
31	RUNX3	chr7:70193749-70194798	GM12878	blood:	n/a	n/a
32	ATF2	chr7:70193730-70194787	GM12878	blood:	n/a	n/a
33	MAX	chr7:70193815-70194207	H1-hESC	embryonic stem cell:	n/a	n/a
34	FOXM1	chr7:70193848-70194740	GM12878	blood:	n/a	n/a
35	POLR2A	chr7:70193892-70194643	GM12878	blood:	n/a	n/a
36	TAF1	chr7:70193875-70194192	H1-hESC	embryonic stem cell:	n/a	n/a
37	YY1	chr7:70193821-70194264	H1-hESC	embryonic stem cell:	n/a	n/a
38	SMC3	chr7:70193777-70194820	GM12878	blood:	n/a	n/a
39	EP300	chr7:70193937-70194557	GM12878	blood:	n/a	chr7:70194393-70194407
40	TCF7L2	chr7:70193772-70194578	HEK293	kidney:	n/a	chr7:70193975-70193984
41	SPI1	chr7:70193945-70194807	GM12878	blood:	n/a	chr7:70194269-70194282 chr7:70194256-70194269
42	STAT1	chr7:70193890-70194077	GM12878	blood:	n/a	chr7:70193979-70193990 chr7:70194033-70194044
43	POLR2A	chr7:70193987-70194306	GM12878	blood:	n/a	n/a
44	CHD1	chr7:70193869-70194679	GM12878	blood:	n/a	n/a
45	EBF1	chr7:70193706-70194834	GM12878	blood:	n/a	chr7:70194434-70194445 chr7:70194351-70194361
46	POLR2A	chr7:70193902-70194055	MCF10A-Er-Src	breast:	n/a	n/a
47	WRNIP1	chr7:70193859-70194458	GM12878	blood:	n/a	n/a
48	EBF1	chr7:70193751-70194136	GM12878	blood:	n/a	n/a
49	RUNX3	chr7:70193782-70194744	GM12878	blood:	n/a	n/a
50	YY1	chr7:70193703-70194413	H1-hESC	embryonic stem cell:	n/a	chr7:70194297-70194308

Variant related genes	Relation type
AUTS2	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10239618	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10247394	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10275631	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10276074	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10282283	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282512	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764092	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12533769	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12666137	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12698920	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13234828	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28664154	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4717546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4718986	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4718987	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718989	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4718990	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6966950	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7790623	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794301	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7805642	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7805679	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532783	chr7:69939570-70245396	Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv3341834	chr7:69968031-70288098	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv532784	chr7:69969631-70204548	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1025164	chr7:70061655-70469358	Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv538931	chr7:70061655-70469358	Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1030496	chr7:70067475-70221743	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1017876	chr7:70073764-70434599	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv519090	chr7:70085934-71071896	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1022747	chr7:70169254-70301285	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv1834837	chr7:70171159-70202993	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv1839975	chr7:70171159-70202993	Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv1812409	chr7:70187264-70206903	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv429771	chr7:70188375-70294296	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv831022	chr7:70189351-70238179	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv916183	chr7:70189900-70220746	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1021274	chr7:70190293-70221743	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1034308	chr7:70190293-70230601	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv538934	chr7:70190293-70230601	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv607433	chr7:70190384-70223193	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	esv1834245	chr7:70193768-70202993	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	esv1836583	chr7:70193768-70202993	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	esv1842252	chr7:70193768-70202993	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:70162200-70201600	Weak transcription	Primary B cells from cord blood	blood
2	chr7:70176200-70201600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:70179800-70201600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr7:70183000-70201600	Weak transcription	Fetal Muscle Leg	muscle
5	chr7:70183200-70200200	Weak transcription	Ovary	ovary
6	chr7:70183200-70201800	Weak transcription	Pancreas	Pancrea
7	chr7:70183400-70195400	Weak transcription	HSMM	muscle
8	chr7:70183600-70197600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:70184400-70195200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr7:70185800-70197600	Weak transcription	HSMMtube	muscle
11	chr7:70186000-70195400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:70186400-70198200	Weak transcription	Dnd41	blood
13	chr7:70187000-70201200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:70190200-70194600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr7:70190200-70201400	Weak transcription	Fetal Kidney	kidney
16	chr7:70190600-70199400	Weak transcription	Left Ventricle	heart
17	chr7:70190600-70199600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:70190600-70201600	Weak transcription	Fetal Intestine Large	intestine
19	chr7:70190800-70194200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr7:70190800-70195400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:70190800-70198000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr7:70190800-70199400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:70191000-70194200	Weak transcription	Esophagus	oesophagus
24	chr7:70191000-70197400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr7:70191400-70195000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:70191600-70195000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr7:70191800-70194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr7:70192200-70197400	Weak transcription	Brain Anterior Caudate	brain
29	chr7:70192200-70200200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:70192400-70196800	Weak transcription	Primary T cells from cord blood	blood
31	chr7:70192400-70197200	Weak transcription	Fetal Thymus	thymus
32	chr7:70192400-70198800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr7:70192400-70199400	Weak transcription	Fetal Heart	heart
34	chr7:70192600-70194400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:70192600-70194800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr7:70193000-70194200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr7:70193000-70194200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:70193000-70195400	Weak transcription	HMEC	breast
39	chr7:70193000-70195600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr7:70193000-70200600	Weak transcription	Liver	Liver
41	chr7:70193200-70196000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:70193400-70194200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr7:70193800-70194200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr7:70193800-70194200	Flanking Active TSS	NHEK	skin
45	chr7:70193800-70194400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:70193800-70194400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr7:70193800-70194400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:70193800-70194400	Active TSS	Duodenum Mucosa	Duodenum
49	chr7:70193800-70194400	Genic enhancers	Fetal Intestine Small	intestine
50	chr7:70193800-70194400	Enhancers	Fetal Lung	lung

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