Variant report

Variant	rs10743789
Chromosome Location	chr12:9769079-9769080
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10771926	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10771927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771929	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771930	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771935	0.89[ASN][1000 genomes]
rs10771936	0.94[ASN][1000 genomes]
rs10771947	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10844160	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844161	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10844191	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10844196	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10844206	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844225	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10844233	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10844269	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11051877	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11051879	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11051959	0.95[ASN][1000 genomes]
rs11052008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11052013	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs11052027	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11052031	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12301481	0.93[ASN][1000 genomes]
rs12308360	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12321613	0.95[ASN][1000 genomes]
rs12580472	0.92[ASN][1000 genomes]
rs1529418	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1529419	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1863876	0.93[ASN][1000 genomes]
rs1987426	0.93[ASN][1000 genomes]
rs2401386	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35721310	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4486710	0.91[ASN][1000 genomes]
rs4763675	0.92[ASN][1000 genomes]
rs4763678	0.87[ASN][1000 genomes]
rs4763715	0.81[ASN][1000 genomes]
rs4763716	0.82[ASN][1000 genomes]
rs4763717	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs5023032	1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60416399	0.93[ASN][1000 genomes]
rs6488042	0.87[ASN][1000 genomes]
rs6488054	0.95[ASN][1000 genomes]
rs66927586	0.93[ASN][1000 genomes]
rs7132715	0.88[ASN][1000 genomes]
rs7138619	0.97[ASN][1000 genomes]
rs72656628	0.91[ASN][1000 genomes]
rs72656629	0.85[ASN][1000 genomes]
rs7301291	0.93[ASN][1000 genomes]
rs7302021	0.86[ASN][1000 genomes]
rs7310367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7311954	0.93[ASN][1000 genomes]
rs7314188	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7954289	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978641	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2757489	chr12:9583455-9810764	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10743789	RP11-726G1.1	cis	Artery Aorta	GTEx
rs10743789	GSG1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9755800-9771200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:9759200-9771200	Weak transcription	Fetal Lung	lung
3	chr12:9764200-9777000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:9766400-9769800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:9767400-9770600	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:9767600-9769400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr12:9767600-9770000	Enhancers	Primary hematopoietic stem cells	blood
8	chr12:9768400-9769800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:9768400-9770400	Enhancers	Primary B cells from cord blood	blood
10	chr12:9768400-9772200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr12:9768400-9772200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr12:9768600-9769400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:9768600-9769600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:9768600-9770200	Enhancers	GM12878-XiMat	blood
15	chr12:9768600-9770400	Enhancers	Thymus	Thymus
16	chr12:9768600-9770600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr12:9768800-9770000	Enhancers	Fetal Thymus	thymus
18	chr12:9768800-9770200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:9768800-9770200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr12:9768800-9770200	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr12:9768800-9770400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr12:9768800-9771000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:9768800-9772800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr12:9768800-9772800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr12:9769000-9769200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:9769000-9770200	Enhancers	Primary T cells from cord blood	blood
27	chr12:9769000-9770600	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr12:9769000-9770800	Enhancers	Dnd41	blood
29	chr12:9769000-9771000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:9769000-9771600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr12:9769000-9773200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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