Variant report

Variant	rs4680421
Chromosome Location	chr3:157934971-157934972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 144 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10470472	0.81[ASN][1000 genomes]
rs10936131	0.88[CEU][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes]
rs10936132	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[EUR][1000 genomes]
rs10936139	0.90[EUR][1000 genomes]
rs1095636	0.92[ASN][1000 genomes]
rs11707386	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11712563	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11715599	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11716327	0.92[CEU][hapmap]
rs11716969	0.89[EUR][1000 genomes]
rs11717618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717923	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[EUR][1000 genomes]
rs11719124	0.90[EUR][1000 genomes]
rs11719153	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1193511	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs1193536	0.87[ASN][1000 genomes]
rs1204957	0.89[ASN][1000 genomes]
rs12053861	0.91[EUR][1000 genomes]
rs12053865	0.91[EUR][1000 genomes]
rs12053869	0.92[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs12485440	0.96[CHD][hapmap];0.86[JPT][hapmap]
rs12496934	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12634807	0.91[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs12636733	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12637649	0.89[EUR][1000 genomes]
rs12639261	0.91[EUR][1000 genomes]
rs12639310	0.91[EUR][1000 genomes]
rs12696067	0.80[CEU][hapmap];0.93[CHD][hapmap];0.80[JPT][hapmap]
rs13059066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1581408	0.80[JPT][hapmap]
rs1608100	0.96[CHD][hapmap];0.80[JPT][hapmap]
rs1609525	0.85[JPT][hapmap]
rs1724666	0.99[ASN][1000 genomes]
rs1724679	0.92[ASN][1000 genomes]
rs1729998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1730029	0.96[ASN][1000 genomes]
rs1730032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1730044	0.91[ASN][1000 genomes]
rs1730099	0.92[CHB][hapmap];0.80[JPT][hapmap];0.96[ASN][1000 genomes]
rs17627933	0.89[EUR][1000 genomes]
rs17683939	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1851062	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1915935	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1918000	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2139696	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682402	0.89[ASN][1000 genomes]
rs2682407	0.99[ASN][1000 genomes]
rs2693540	0.84[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2693546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs34434866	0.91[EUR][1000 genomes]
rs4346508	0.96[CHD][hapmap];0.85[JPT][hapmap]
rs4402974	0.92[CEU][hapmap]
rs4431056	0.80[JPT][hapmap]
rs4680412	0.85[JPT][hapmap]
rs4680413	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4680425	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4680428	0.91[EUR][1000 genomes]
rs4680432	0.91[EUR][1000 genomes]
rs56123505	0.91[EUR][1000 genomes]
rs57665991	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58195752	0.90[EUR][1000 genomes]
rs58925169	0.91[EUR][1000 genomes]
rs60962704	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441193	0.92[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs6762706	0.96[ASN][1000 genomes]
rs6767494	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs6772246	0.90[EUR][1000 genomes]
rs6784968	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs6790608	0.80[JPT][hapmap]
rs6800218	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6800853	0.91[EUR][1000 genomes]
rs6803630	0.96[CHD][hapmap];0.80[JPT][hapmap]
rs6807468	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs696715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs698975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs698976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs698977	0.99[ASN][1000 genomes]
rs698979	0.99[ASN][1000 genomes]
rs698981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs698982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs698983	0.96[ASN][1000 genomes]
rs698984	0.99[ASN][1000 genomes]
rs698985	0.99[ASN][1000 genomes]
rs698992	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs699918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs699923	0.99[ASN][1000 genomes]
rs699925	0.99[ASN][1000 genomes]
rs699926	0.99[ASN][1000 genomes]
rs73164102	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73166358	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73168723	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73168799	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73170303	0.92[EUR][1000 genomes]
rs73170306	0.91[EUR][1000 genomes]
rs73170310	0.91[EUR][1000 genomes]
rs73170326	0.91[EUR][1000 genomes]
rs73170337	0.91[EUR][1000 genomes]
rs73170339	0.91[EUR][1000 genomes]
rs73170346	0.91[EUR][1000 genomes]
rs73170364	0.91[EUR][1000 genomes]
rs73170373	0.91[EUR][1000 genomes]
rs73170375	0.91[EUR][1000 genomes]
rs73172105	0.90[EUR][1000 genomes]
rs7614572	0.86[JPT][hapmap]
rs7617666	0.81[CEU][hapmap]
rs7622971	0.86[JPT][hapmap]
rs7624303	1.00[CEU][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7630176	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs7640075	0.91[EUR][1000 genomes]
rs7641036	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs7652970	0.89[EUR][1000 genomes]
rs827104	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs827130	0.91[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs827139	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs827141	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs827142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs827145	0.95[ASN][1000 genomes]
rs827146	0.96[ASN][1000 genomes]
rs827147	0.96[ASN][1000 genomes]
rs827149	0.96[ASN][1000 genomes]
rs827153	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs827155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs827157	0.96[ASN][1000 genomes]
rs827160	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs827162	0.91[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs827168	0.91[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs827170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs827173	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs827174	0.92[ASN][1000 genomes]
rs827801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs827805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs862352	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs864331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs864876	0.96[ASN][1000 genomes]
rs866657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9290021	0.80[JPT][hapmap]
rs9814942	0.86[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv829768	chr3:157832878-158012070	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv1819976	chr3:157923372-157945591	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	nsv916910	chr3:157926799-158183372	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4680421	RP11-538P18.2	cis	Artery Tibial	GTEx
rs4680421	RP11-538P18.2	cis	lung	GTEx
rs4680421	RP11-538P18.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4680421	RSRC1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157914200-157984400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:157918000-157938000	Weak transcription	Left Ventricle	heart
3	chr3:157919200-157958000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr3:157919800-157952800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:157920000-157935000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:157920200-157957000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:157921000-157937600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:157921200-157936000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:157921600-157936400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr3:157922000-157950000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:157925600-157936000	Weak transcription	Primary T cells from cord blood	blood
12	chr3:157926400-157938000	Weak transcription	Ovary	ovary
13	chr3:157927000-157945200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:157927000-157952600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:157927000-157968800	Weak transcription	Psoas Muscle	Psoas
16	chr3:157927600-157937600	Weak transcription	Primary B cells from cord blood	blood
17	chr3:157928200-157956200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:157929000-157946800	Weak transcription	Dnd41	blood
19	chr3:157930600-157936400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:157931000-157937600	Weak transcription	Stomach Mucosa	stomach
21	chr3:157933000-157936600	Weak transcription	Fetal Heart	heart
22	chr3:157933800-157957200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:157934800-157938800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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