Variant report

Variant	rs6954179
Chromosome Location	chr7:47802663-47802664
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	JUND	chr7:47802587-47803711	A549	lung:	n/a	chr7:47803401-47803412
2	EP300	chr7:47802370-47803711	SK-N-SH_RA	brain:	n/a	chr7:47802404-47802420 chr7:47802950-47802964
3	JUND	chr7:47802525-47803810	SK-N-SH	brain:	n/a	chr7:47803401-47803412
4	FOXA2	chr7:47802409-47804069	HepG2	liver:	n/a	n/a
5	EP300	chr7:47801845-47805996	SK-N-SH	brain:	n/a	chr7:47802404-47802420 chr7:47804435-47804443 chr7:47802950-47802964
6	TEAD4	chr7:47802353-47803745	SK-N-SH	brain:	n/a	n/a
7	MYBL2	chr7:47802517-47803839	HepG2	liver:	n/a	n/a
8	MAX	chr7:47802480-47803602	HepG2	liver:	n/a	n/a
9	PBX3	chr7:47802433-47803741	SK-N-SH	brain:	n/a	n/a
10	RAD21	chr7:47802635-47803656	SK-N-SH_RA	brain:	n/a	n/a
11	HEY1	chr7:47802310-47803224	HepG2	liver:	n/a	chr7:47802553-47802562 chr7:47802398-47802407
12	MXI1	chr7:47802607-47803601	HepG2	liver:	n/a	n/a
13	BCL3	chr7:47802221-47803718	A549	lung:	n/a	chr7:47802944-47802953
14	HDAC2	chr7:47802615-47803709	HepG2	liver:	n/a	chr7:47803594-47803608
15	MAX	chr7:47802595-47803582	Hela-S3	cervix:	n/a	n/a
16	EP300	chr7:47802461-47803840	A549	lung:	n/a	chr7:47802950-47802964
17	MAX	chr7:47802231-47803720	SK-N-SH	brain:	n/a	n/a
18	NFIC	chr7:47802498-47803695	HepG2	liver:	n/a	n/a
19	POLR2A	chr7:47802638-47802730	A549	lung:	n/a	n/a
20	EP300	chr7:47802171-47803853	A549	lung:	n/a	chr7:47802404-47802420 chr7:47802950-47802964
21	GATA3	chr7:47802588-47803603	SH-SY5Y	brain:	n/a	n/a
22	GATA2	chr7:47802436-47803644	SH-SY5Y	brain:	n/a	n/a
23	GATA3	chr7:47802404-47803830	SK-N-SH	brain:	n/a	n/a
24	GATA3	chr7:47802237-47803854	A549	lung:	n/a	chr7:47802401-47802408
25	REST	chr7:47802552-47803571	A549	lung:	n/a	n/a
26	POLR2A	chr7:47802186-47803097	HepG2	liver:	n/a	n/a
27	PBX3	chr7:47802256-47803682	SK-N-SH	brain:	n/a	n/a
28	FOSL2	chr7:47802658-47803649	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr7:47802063-47803709	HepG2	liver:	n/a	n/a
30	MAX	chr7:47802243-47803766	A549	lung:	n/a	n/a
31	ELK1	chr7:47802576-47802739	Hela-S3	cervix:	n/a	n/a
32	TCF12	chr7:47802610-47803620	A549	lung:	n/a	chr7:47802829-47802836
33	RAD21	chr7:47802478-47803754	A549	lung:	n/a	n/a
34	JUND	chr7:47802563-47803744	SK-N-SH	brain:	n/a	chr7:47803401-47803412
35	ATF3	chr7:47802645-47803677	A549	lung:	n/a	n/a
36	CTCF	chr7:47802640-47802790	WERI-Rb-1	eye:	n/a	n/a
37	PBX3	chr7:47802652-47803592	A549	lung:	n/a	n/a
38	TEAD4	chr7:47802614-47803729	HepG2	liver:	n/a	n/a
39	GATA3	chr7:47802527-47803740	MCF-7	breast:	n/a	n/a
40	REST	chr7:47802497-47803701	A549	lung:	n/a	chr7:47802521-47802531
41	MEF2A	chr7:47802574-47803752	SK-N-SH	brain:	n/a	chr7:47802765-47802773 chr7:47803610-47803621
42	MAX	chr7:47802149-47803793	HepG2	liver:	n/a	n/a
43	NFIC	chr7:47802442-47803752	SK-N-SH	brain:	n/a	n/a
44	NFIC	chr7:47802214-47803803	HepG2	liver:	n/a	n/a
45	RAD21	chr7:47802633-47803681	HepG2	liver:	n/a	n/a
46	RXRA	chr7:47802456-47803716	SK-N-SH	brain:	n/a	chr7:47803374-47803387 chr7:47803501-47803515 chr7:47803373-47803387
47	BCL3	chr7:47802544-47803831	A549	lung:	n/a	chr7:47802944-47802953
48	SP1	chr7:47802190-47803780	A549	lung:	n/a	chr7:47802449-47802463
49	RXRA	chr7:47802508-47803762	SK-N-SH	brain:	n/a	chr7:47803374-47803387 chr7:47803501-47803515 chr7:47803373-47803387
50	FOXA1	chr7:47802662-47803780	HepG2	liver:	n/a	chr7:47803429-47803444 chr7:47803447-47803462

Variant related genes	Relation type
LINC00525	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10261383	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10276803	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10807948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10951927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11767747	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12702380	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12702381	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12702382	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12702383	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13223384	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13223474	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13232562	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13232587	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13232795	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236333	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13236472	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13236558	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13236571	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13236668	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34321500	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34368666	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34667448	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34826626	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34893998	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34894454	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34925936	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35527194	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35550210	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35638709	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35916540	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4724634	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4724635	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4724636	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4724637	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4724638	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5004318	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5004319	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5004320	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5004321	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5004322	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5004323	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5004325	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5004326	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6463437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6463438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6463439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6463440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6463441	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6463442	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66472878	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6953339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6953403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953684	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6953875	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71546001	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71546002	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7791909	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807530	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7811726	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1018608	chr7:47708525-47831535	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1022906	chr7:47709936-47831535	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1015163	chr7:47734913-47832389	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv538831	chr7:47734913-47832389	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv830990	chr7:47767540-47837584	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47797800-47802800	Weak transcription	Placenta	Placenta
2	chr7:47798000-47803000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:47798400-47802800	Weak transcription	Fetal Kidney	kidney
4	chr7:47798400-47802800	Weak transcription	Fetal Lung	lung
5	chr7:47798400-47802800	Weak transcription	Fetal Muscle Leg	muscle
6	chr7:47798600-47802800	Weak transcription	Adipose Nuclei	Adipose
7	chr7:47798600-47812200	Weak transcription	Aorta	Aorta
8	chr7:47801400-47803000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:47801400-47803800	Enhancers	NHDF-Ad	bronchial
10	chr7:47801800-47804600	Enhancers	Liver	Liver
11	chr7:47802000-47803000	Flanking Active TSS	HepG2	liver
12	chr7:47802000-47804200	Enhancers	Fetal Intestine Small	intestine
13	chr7:47802000-47804400	Enhancers	NH-A	brain
14	chr7:47802000-47804600	Enhancers	NHLF	lung
15	chr7:47802000-47804800	Enhancers	Fetal Intestine Large	intestine
16	chr7:47802200-47803000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:47802200-47803800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:47802200-47803800	Enhancers	Osteobl	bone
19	chr7:47802200-47804400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:47802200-47805800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:47802400-47802800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:47802400-47802800	Enhancers	Spleen	Spleen
23	chr7:47802400-47803000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:47802400-47803000	Flanking Active TSS	A549	lung
25	chr7:47802400-47803200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr7:47802400-47803200	Enhancers	Fetal Muscle Trunk	muscle
27	chr7:47802400-47803200	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr7:47802400-47803400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:47802400-47803400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:47802400-47803400	Enhancers	Primary B cells from peripheral blood	blood
31	chr7:47802400-47803400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr7:47802400-47803400	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr7:47802400-47803600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:47802400-47803600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:47802400-47803600	Enhancers	Stomach Mucosa	stomach
36	chr7:47802400-47803600	Enhancers	HMEC	breast
37	chr7:47802400-47803600	Enhancers	HSMMtube	muscle
38	chr7:47802400-47803800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:47802400-47803800	Enhancers	HSMM	muscle
40	chr7:47802600-47802800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr7:47802600-47802800	Enhancers	Pancreas	Pancrea
42	chr7:47802600-47802800	Enhancers	Stomach Smooth Muscle	stomach
43	chr7:47802600-47803000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:47802600-47803000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr7:47802600-47803000	Enhancers	Duodenum Mucosa	Duodenum
46	chr7:47802600-47803000	Enhancers	Small Intestine	intestine
47	chr7:47802600-47803000	Enhancers	GM12878-XiMat	blood
48	chr7:47802600-47803200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:47802600-47803200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr7:47802600-47803400	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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