Variant report

Variant	rs10506398
Chromosome Location	chr12:60111326-60111327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10431557	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10506399	0.86[CHB][hapmap];0.88[GIH][hapmap]
rs10877338	0.86[CHB][hapmap]
rs11173126	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]
rs11173133	0.84[CEU][hapmap]
rs11173159	0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs12227244	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12227270	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12231311	0.91[CHB][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs12231693	0.89[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12231740	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12232002	0.91[CHB][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs12816935	0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17649424	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs17650311	0.91[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap]
rs1795884	0.81[CHB][hapmap]
rs1795896	0.85[CHB][hapmap]
rs2706306	0.86[CHB][hapmap]
rs2706309	0.86[CHB][hapmap]
rs2706319	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs2711655	0.86[CHB][hapmap]
rs2711656	0.85[CHB][hapmap]
rs2711659	0.81[CHB][hapmap]
rs2711668	0.85[CHB][hapmap]
rs3763980	0.91[CHB][hapmap];0.82[GIH][hapmap]
rs3847655	0.85[CEU][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61174819	0.83[EUR][1000 genomes]
rs7133415	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs7136019	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7303876	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs995342	0.89[ASW][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];0.97[MKK][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv2829972	chr12:60079404-60111653	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10506398	SLC16A7	cis	lymphoblastoid	seeQTL
rs10506398	KIF5A	cis	cerebellum	SCAN
rs10506398	SLC16A7	Cis_1M	lymphoblastoid	RTeQTL
rs10506398	DCTN2	cis	cerebellum	SCAN
rs10506398	SLC16A7	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 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	chr12:60095400-60114400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:60098000-60117000	Weak transcription	Psoas Muscle	Psoas
8	chr12:60099200-60126600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr12:60099400-60130400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr12:60099600-60143200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr12:60100000-60175200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:60100400-60126400	Weak transcription	Primary B cells from cord blood	blood
13	chr12:60100600-60127200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:60101800-60122000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:60103400-60111600	Weak transcription	GM12878-XiMat	blood
16	chr12:60104200-60138000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:60105000-60111600	Weak transcription	Thymus	Thymus
18	chr12:60105000-60112200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:60105600-60129200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:60106800-60117800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:60108800-60112600	Enhancers	Liver	Liver
22	chr12:60109400-60121800	Weak transcription	Right Ventricle	heart
23	chr12:60109400-60126600	Weak transcription	Primary T cells from cord blood	blood
24	chr12:60110200-60141400	Weak transcription	Dnd41	blood
25	chr12:60111000-60111400	Enhancers	Fetal Heart	heart
26	chr12:60111000-60111600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:60111000-60112600	Enhancers	Adipose Nuclei	Adipose

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