Variant report

Variant	rs12232002
Chromosome Location	chr12:60139822-60139823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10431557	0.91[CHB][hapmap]
rs10506398	0.91[CHB][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs10506399	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877338	0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs11173124	0.89[ASN][1000 genomes]
rs11173126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173133	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11173134	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11173137	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11173158	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11173159	0.90[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12227214	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12227244	0.82[CEU][hapmap];0.91[CHB][hapmap];0.83[AFR][1000 genomes]
rs12227270	0.91[CHB][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs12231311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12231693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12231740	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12812799	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816935	0.90[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs17572877	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17572912	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17649424	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17650311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1795884	0.91[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs1795896	0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2365317	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2365318	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2706295	0.91[ASN][1000 genomes]
rs2706306	0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2706309	0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2706319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2711655	0.95[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2711656	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs2711659	0.90[CHB][hapmap];0.91[ASN][1000 genomes]
rs2711668	0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2711670	0.90[ASN][1000 genomes]
rs2711672	0.90[ASN][1000 genomes]
rs2711677	0.90[ASN][1000 genomes]
rs2711691	0.91[ASN][1000 genomes]
rs34264510	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34639075	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34785387	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35218918	0.86[ASN][1000 genomes]
rs35365387	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35518979	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35971116	0.86[ASN][1000 genomes]
rs3763980	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847655	0.81[AFR][1000 genomes]
rs4583011	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56682442	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61174819	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581274	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66802005	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66861118	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68028492	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7136019	0.83[EUR][1000 genomes]
rs7303876	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7979504	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9705733	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9788077	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs995342	0.85[CEU][hapmap]

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	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
3	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
4	nsv899133	chr12:60135504-60202218	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12232002	SLC16A7	Cis_1M	lymphoblastoid	RTeQTL
rs12232002	SLC16A7	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60099600-60143200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr12:60100000-60175200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:60110200-60141400	Weak transcription	Dnd41	blood
4	chr12:60113000-60143600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:60124000-60168800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr12:60127800-60143000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:60127800-60143200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr12:60128200-60143000	Weak transcription	Gastric	stomach
9	chr12:60128400-60140000	Weak transcription	Thymus	Thymus
10	chr12:60130800-60142800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:60130800-60172200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr12:60131000-60186000	Weak transcription	Pancreas	Pancrea
13	chr12:60132400-60140200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:60132400-60165600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:60136200-60140000	Weak transcription	Primary T cells from cord blood	blood
16	chr12:60136400-60140400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:60136400-60142800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:60137400-60161000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:60137800-60141000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:60138000-60141200	Weak transcription	Ovary	ovary
21	chr12:60138000-60147000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:60138400-60141800	Strong transcription	Primary B cells from cord blood	blood
23	chr12:60138600-60168400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:60138800-60141600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:60138800-60141600	Weak transcription	Right Ventricle	heart
26	chr12:60138800-60142200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:60138800-60142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:60138800-60143200	Weak transcription	Left Ventricle	heart
29	chr12:60138800-60173200	Weak transcription	Aorta	Aorta
30	chr12:60139000-60144600	Weak transcription	Adipose Nuclei	Adipose
31	chr12:60139400-60141800	Weak transcription	GM12878-XiMat	blood

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