Variant report

Variant	rs4779529
Chromosome Location	chr15:31750268-31750269
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	TCF12	chr15:31749965-31750386	GM12878	blood:	n/a	chr15:31750160-31750167
2	POU2F2	chr15:31750012-31750522	GM12891	blood:	n/a	n/a
3	MAX	chr15:31750107-31750487	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOSL1	chr15:31750124-31750527	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZNF143	chr15:31750113-31750515	H1-hESC	embryonic stem cell:	n/a	n/a
6	RUNX3	chr15:31750040-31750353	GM12878	blood:	n/a	n/a
7	MAX	chr15:31750109-31750466	H1-hESC	embryonic stem cell:	n/a	n/a
8	FOXM1	chr15:31750030-31750389	GM12878	blood:	n/a	n/a
9	CTCF	chr15:31750120-31750270	GM12875	blood:	n/a	n/a
10	ZNF143	chr15:31750195-31750485	GM12878	blood:	n/a	n/a
11	TCF12	chr15:31750032-31750296	H1-hESC	embryonic stem cell:	n/a	chr15:31750160-31750167
12	RUNX3	chr15:31749957-31750460	GM12878	blood:	n/a	n/a
13	E2F6	chr15:31750032-31750452	H1-hESC	embryonic stem cell:	n/a	n/a
14	FOSL1	chr15:31750132-31750543	H1-hESC	embryonic stem cell:	n/a	n/a
15	TCF3	chr15:31750048-31750424	GM12878	blood:	n/a	chr15:31750146-31750160

No.	Distal block	Cell Line	Cell type
1	chr15:31747904..31750478-chr15:31754531..31757245,2	MCF-7	breast:
2	chr15:31748477..31753108-chr15:31776889..31783172,7	MCF-7	breast:
3	chr15:31731861..31735385-chr15:31748681..31751856,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259696	TF binding region

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1017720	0.82[EUR][1000 genomes]
rs1077169	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10851568	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10851569	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11071070	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11071075	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11071076	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12148161	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12148181	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439019	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12439195	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439214	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439216	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439310	0.80[EUR][1000 genomes]
rs12440316	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12441399	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12441529	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12441571	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12441588	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12441627	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12443255	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12443432	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592099	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592342	0.96[ASN][1000 genomes]
rs12592371	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12595455	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1380235	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17228303	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17228317	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17815977	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2008020	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2125617	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2125618	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2219508	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2338683	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28366602	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28367155	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28379435	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28392564	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28403178	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28421719	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28470561	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28533482	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28549906	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28557161	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28579624	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28619436	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28623261	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28633343	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28633823	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28644187	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28655541	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28668028	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28673491	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28683761	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28685794	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28687203	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28696791	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28703622	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28716634	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28825540	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28896251	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35643888	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4238555	0.96[ASN][1000 genomes]
rs4401013	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4414458	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4451913	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4497646	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4611410	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4779528	0.96[ASN][1000 genomes]
rs4779530	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4779531	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4779534	0.87[EUR][1000 genomes]
rs4779881	0.98[ASN][1000 genomes]
rs4779882	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55806858	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56008248	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56332002	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56349550	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62037907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493688	0.81[EUR][1000 genomes]
rs6493689	0.80[EUR][1000 genomes]
rs7403275	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7403458	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs755809	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs755812	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8023660	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8023664	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8023790	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8035018	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8038667	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8038953	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8040186	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs971330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs971331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs971332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1051589	chr15:31728004-31972706	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv542320	chr15:31728004-31972706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv469633	chr15:31731003-31904613	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv482330	chr15:31731003-31904613	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv903844	chr15:31736091-31781988	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1046271	chr15:31741255-31795961	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv9233	chr15:31749686-31752999	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31747000-31750800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr15:31748000-31751000	Weak transcription	Primary T cells from cord blood	blood
3	chr15:31748000-31751000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:31748200-31750400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr15:31748200-31750800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr15:31748200-31750800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:31748200-31750800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:31748200-31751000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:31748200-31751000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr15:31748400-31751800	Enhancers	A549	lung
11	chr15:31748600-31751600	Enhancers	Esophagus	oesophagus
12	chr15:31748600-31751800	Enhancers	NHEK	skin
13	chr15:31748600-31752000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:31748800-31750600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:31748800-31750600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:31748800-31750800	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr15:31748800-31751000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:31748800-31751000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:31748800-31751200	Enhancers	Adipose Nuclei	Adipose
20	chr15:31748800-31751400	Enhancers	HSMM	muscle
21	chr15:31748800-31751400	Enhancers	HSMMtube	muscle
22	chr15:31749000-31750400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:31749000-31750600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr15:31749000-31750600	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr15:31749000-31750600	Enhancers	NHLF	lung
26	chr15:31749000-31751800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:31749200-31750400	Enhancers	GM12878-XiMat	blood
28	chr15:31749200-31750600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:31749200-31751400	Enhancers	NH-A	brain
30	chr15:31749200-31752000	Enhancers	HMEC	breast
31	chr15:31749200-31753200	Weak transcription	Left Ventricle	heart
32	chr15:31749200-31764000	Weak transcription	Right Atrium	heart
33	chr15:31749400-31751800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:31749600-31750800	Weak transcription	Fetal Heart	heart
35	chr15:31749600-31751200	Enhancers	Primary B cells from cord blood	blood
36	chr15:31749600-31753200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr15:31749600-31753600	Enhancers	Primary B cells from peripheral blood	blood
38	chr15:31749800-31751000	Weak transcription	Colonic Mucosa	Colon
39	chr15:31749800-31751400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:31749800-31751400	Enhancers	NHDF-Ad	bronchial
41	chr15:31749800-31751800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:31749800-31751800	Enhancers	Osteobl	bone
43	chr15:31749800-31752200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:31750000-31750400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr15:31750000-31751400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:31750000-31751400	Enhancers	Fetal Thymus	thymus
47	chr15:31750000-31751600	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr15:31750200-31750400	Enhancers	Gastric	stomach
49	chr15:31750200-31750400	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr15:31750200-31750400	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links