Variant report

Variant	rs10936145
Chromosome Location	chr3:158193136-158193137
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10936131	0.84[ASW][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10936132	0.82[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10936139	0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10936143	0.84[ASW][hapmap];0.95[CEU][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10936144	0.89[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707386	0.84[ASW][hapmap];0.94[CHD][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11708784	0.90[CEU][hapmap];0.90[GIH][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11710813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712563	0.80[AMR][1000 genomes]
rs11714821	0.89[CHB][hapmap]
rs11716327	0.84[ASW][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs11716969	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11717923	1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs11719124	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11719153	1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs1193511	0.90[JPT][hapmap]
rs12053861	0.80[AMR][1000 genomes]
rs12053865	0.80[AMR][1000 genomes]
rs12053869	0.89[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs12491598	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12492884	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12493128	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12494926	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12495085	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12496934	0.84[ASW][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12631704	0.95[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12634807	0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs12636733	0.84[ASW][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs12637649	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12639261	0.80[AMR][1000 genomes]
rs12639310	0.80[AMR][1000 genomes]
rs16829104	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17627933	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17628958	0.91[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17628988	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17683939	0.90[JPT][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap]
rs17684859	0.91[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1918000	0.82[AMR][1000 genomes]
rs28431969	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34434866	0.80[AMR][1000 genomes]
rs4402974	0.84[ASW][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs4680428	0.80[AMR][1000 genomes]
rs4680432	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4680435	0.84[ASW][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4680441	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4680444	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55720154	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55765541	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55842512	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56123505	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs58195752	0.80[AMR][1000 genomes]
rs58925169	0.80[AMR][1000 genomes]
rs6441193	0.90[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs6767494	0.89[JPT][hapmap]
rs6783284	1.00[CHB][hapmap]
rs6784511	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6784968	0.84[ASW][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs6788907	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6799272	0.89[CHB][hapmap]
rs6800853	0.80[AMR][1000 genomes]
rs6806967	0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6807468	0.82[AMR][1000 genomes]
rs73154304	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73154306	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73154307	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73154309	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73154313	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73154314	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73154326	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73154329	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73154331	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73154340	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73168723	0.80[AMR][1000 genomes]
rs73168799	0.82[AMR][1000 genomes]
rs73170303	0.80[AMR][1000 genomes]
rs73170306	0.80[AMR][1000 genomes]
rs73170310	0.80[AMR][1000 genomes]
rs73170326	0.80[AMR][1000 genomes]
rs73170337	0.80[AMR][1000 genomes]
rs73170339	0.80[AMR][1000 genomes]
rs73170346	0.80[AMR][1000 genomes]
rs73170364	0.80[AMR][1000 genomes]
rs73170373	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73170375	0.80[AMR][1000 genomes]
rs73172105	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73172114	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73172119	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73172134	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613528	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7640075	0.80[AMR][1000 genomes]
rs7641036	1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7649463	0.89[CHB][hapmap]
rs7652970	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs827130	0.90[JPT][hapmap]
rs827162	0.90[JPT][hapmap]
rs827168	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10936145	VEPH1	cis	cerebellum	SCAN
rs10936145	SHOX2	cis	lymphoblastoid	seeQTL
rs10936145	RP11-538P18.2	cis	Nerve Tibial	GTEx
rs10936145	RP11-538P18.2	cis	Artery Tibial	GTEx
rs10936145	RSRC1	cis	Adipose Subcutaneous	GTEx
rs10936145	RSRC1	cis	normal skin	skin_eQTL
rs10936145	RP11-538P18.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10936145	SSR3	cis	cerebellum	SCAN
rs10936145	RSRC1	Cis_1M	lymphoblastoid	RTeQTL
rs10936145	RP11-538P18.2	cis	Adipose Subcutaneous	GTEx
rs10936145	TIPARP	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158190200-158201000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:158190600-158195600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:158191000-158193600	Weak transcription	Dnd41	blood
4	chr3:158192400-158194200	Weak transcription	Rectal Smooth Muscle	rectum

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