Variant report

Variant	rs1978779
Chromosome Location	chr3:158211291-158211292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10936133	0.82[JPT][hapmap]
rs10936134	0.82[JPT][hapmap]
rs10936146	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1095642	0.82[JPT][hapmap];0.87[YRI][hapmap]
rs11709804	0.82[JPT][hapmap]
rs11714821	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11714869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719037	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1193509	0.81[JPT][hapmap]
rs1193510	0.81[JPT][hapmap]
rs12494098	0.82[JPT][hapmap]
rs12496767	0.96[CEU][hapmap];0.89[CHB][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12629587	0.81[JPT][hapmap]
rs12632998	0.82[JPT][hapmap]
rs12637678	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12638438	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1369562	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1595028	0.96[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs1595029	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1595030	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1656366	0.83[JPT][hapmap]
rs1656376	0.82[JPT][hapmap]
rs1714507	0.82[JPT][hapmap]
rs1714518	0.80[CEU][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1730040	0.82[JPT][hapmap]
rs1978781	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap]
rs2222326	0.82[JPT][hapmap]
rs2362965	0.81[JPT][hapmap]
rs2362969	0.84[YRI][hapmap]
rs2682406	0.82[JPT][hapmap]
rs2693542	0.82[JPT][hapmap]
rs3845981	0.82[JPT][hapmap]
rs4289388	0.84[YRI][hapmap];0.80[ASN][1000 genomes]
rs4309677	0.82[JPT][hapmap]
rs4431160	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4510417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680431	0.85[JPT][hapmap]
rs4680436	0.84[CEU][hapmap]
rs4680437	0.85[CEU][hapmap];0.84[YRI][hapmap]
rs4680439	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441188	0.81[JPT][hapmap]
rs6441195	0.85[CEU][hapmap]
rs6441198	0.80[ASN][1000 genomes]
rs6441201	0.96[CEU][hapmap];0.83[CHB][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6441203	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441204	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441206	0.89[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6762860	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6767008	0.82[JPT][hapmap]
rs6774461	0.81[JPT][hapmap]
rs6778202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6778370	0.81[JPT][hapmap]
rs6780896	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6783284	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6787172	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6788703	0.82[JPT][hapmap]
rs6791431	0.81[JPT][hapmap]
rs6795376	0.96[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6800887	0.84[CEU][hapmap];0.83[YRI][hapmap]
rs7610691	0.84[CEU][hapmap]
rs7610713	0.85[JPT][hapmap]
rs7620927	0.96[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7623732	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7630443	0.88[CEU][hapmap]
rs7632059	0.83[YRI][hapmap]
rs7639678	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7641954	0.85[CEU][hapmap];0.80[ASN][1000 genomes]
rs7648196	0.82[JPT][hapmap]
rs7648618	0.96[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7649463	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs827106	0.81[JPT][hapmap]
rs827127	0.82[JPT][hapmap]
rs827129	0.81[JPT][hapmap]
rs827131	0.82[JPT][hapmap]
rs827134	0.82[JPT][hapmap]
rs827135	0.83[YRI][hapmap]
rs827164	0.82[JPT][hapmap]
rs864332	0.81[JPT][hapmap]
rs939117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9810114	0.96[CEU][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9810887	0.96[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9812624	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9819134	0.96[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9823076	0.87[CEU][hapmap];0.80[JPT][hapmap]
rs9827781	0.85[JPT][hapmap]
rs9835244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9857535	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9858318	0.96[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9859129	0.96[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9865460	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9867617	0.89[JPT][hapmap]
rs9870802	0.85[CEU][hapmap]
rs9872889	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9880806	0.82[JPT][hapmap]
rs9883657	0.96[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]

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	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
2	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS 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	37 gene(s)	inside rSNPs	diseases
4	nsv1013046	chr3:158176582-158244606	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1014557	chr3:158176582-158251602	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv877690	chr3:158184263-158296916	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1978779	RP11-538P18.2	cis	Artery Tibial	GTEx
rs1978779	RP11-538P18.2	cis	Skin Sun Exposed Lower leg	GTEx
rs1978779	RSRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158207200-158221400	Weak transcription	Ovary	ovary
2	chr3:158210200-158211600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:158210600-158211400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:158210800-158211600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:158211200-158212600	Weak transcription	K562	blood
6	chr3:158211200-158215200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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