Variant report

Variant	rs11173126
Chromosome Location	chr12:60124089-60124090
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10431557	0.95[CEU][hapmap];0.91[CHB][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs10506398	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10506399	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877338	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs10877342	0.83[CHD][hapmap]
rs11173124	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11173133	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173134	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173137	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173158	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11173159	0.91[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12227214	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12227244	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs12227270	0.87[CEU][hapmap];0.91[CHB][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs12231311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12231693	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12231740	0.91[CHB][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs12232002	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12812799	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12816935	0.94[CHB][hapmap]
rs17572877	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17572912	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17649424	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650311	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795884	0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs1795896	0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2365317	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2365318	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2706295	0.90[ASN][1000 genomes]
rs2706306	0.95[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2706309	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs2706319	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2711655	0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2711656	0.95[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2711659	0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[ASN][1000 genomes]
rs2711668	0.95[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2711670	0.91[ASN][1000 genomes]
rs2711672	0.91[ASN][1000 genomes]
rs2711677	0.91[ASN][1000 genomes]
rs2711691	0.90[ASN][1000 genomes]
rs34264510	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34639075	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34785387	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35218918	0.85[ASN][1000 genomes]
rs35365387	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35518979	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35971116	0.84[ASN][1000 genomes]
rs3763980	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4583011	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56682442	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61174819	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581274	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66802005	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66861118	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68028492	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7133415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303876	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979504	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9705733	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9788077	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv899131	chr12:59942122-60124089	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3365928	chr12:60042531-60343212	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv899132	chr12:60087572-60211476	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11173126	SLC16A7	cis	multi-tissue	Pritchard
rs11173126	SLC16A7	Cis_1M	lymphoblastoid	RTeQTL
rs11173126	RP11-813P10.2	cis	Esophagus Muscularis	GTEx
rs11173126	RP11-813P10.2	cis	Whole Blood	GTEx
rs11173126	KIF5A	cis	cerebellum	SCAN
rs11173126	SLC16A7	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60069600-60131400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr12:60089400-60126000	Weak transcription	Left Ventricle	heart
3	chr12:60093800-60126600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:60094000-60127200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:60094200-60127200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:60099200-60126600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:60099400-60130400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:60099600-60143200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr12:60100000-60175200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:60100400-60126400	Weak transcription	Primary B cells from cord blood	blood
11	chr12:60100600-60127200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:60104200-60138000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:60105600-60129200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:60109400-60126600	Weak transcription	Primary T cells from cord blood	blood
15	chr12:60110200-60141400	Weak transcription	Dnd41	blood
16	chr12:60112600-60126800	Weak transcription	Adipose Nuclei	Adipose
17	chr12:60113000-60143600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:60120200-60127000	Weak transcription	Gastric	stomach
19	chr12:60120600-60130200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:60122200-60127000	Weak transcription	Right Ventricle	heart
21	chr12:60122600-60127000	Weak transcription	Thymus	Thymus
22	chr12:60124000-60127000	Weak transcription	Aorta	Aorta
23	chr12:60124000-60168800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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