Variant report

Variant	rs3026243
Chromosome Location	chr12:9183400-9183401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11048494	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11048496	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11502446	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12303154	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12322917	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12423652	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12426061	0.82[CHB][hapmap]
rs12427063	0.82[CHB][hapmap]
rs12811795	0.96[ASN][1000 genomes]
rs12816157	0.99[ASN][1000 genomes]
rs12819409	0.96[ASN][1000 genomes]
rs12819575	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12822685	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12826978	0.81[JPT][hapmap]
rs12827501	0.99[ASN][1000 genomes]
rs17730331	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17730391	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1805668	0.99[ASN][1000 genomes]
rs1805669	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1805672	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs1805673	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs1805674	0.81[JPT][hapmap]
rs1805675	0.81[JPT][hapmap]
rs1805707	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377678	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2377679	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2377680	0.99[ASN][1000 genomes]
rs2889705	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3026244	0.99[ASN][1000 genomes]
rs3026251	0.81[JPT][hapmap]
rs34533518	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34651717	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34722215	0.93[ASN][1000 genomes]
rs34920912	0.98[ASN][1000 genomes]
rs35176717	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35377225	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35557651	0.99[ASN][1000 genomes]
rs36061702	0.98[ASN][1000 genomes]
rs4883206	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4883208	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4883209	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56083774	0.95[ASN][1000 genomes]
rs56143043	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56350793	0.99[ASN][1000 genomes]
rs60267183	0.99[ASN][1000 genomes]
rs61916006	0.99[ASN][1000 genomes]
rs61916012	0.80[ASN][1000 genomes]
rs7136274	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7302472	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7311267	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7311509	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs759468	0.99[ASN][1000 genomes]
rs759469	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs759470	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7953214	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7957626	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3026243	APOLD1	cis	parietal	SCAN
rs3026243	CLEC6A	cis	cerebellum	SCAN
rs3026243	KLRG1	cis	cerebellum	SCAN
rs3026243	POU5F1P3	cis	parietal	SCAN
rs3026243	MAGOHB	cis	parietal	SCAN
rs3026243	KLRG1	cis	multi-tissue	Pritchard
rs3026243	RIMKLB	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9174800-9185800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:9175200-9185800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr12:9178400-9185000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:9178400-9216400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:9178800-9184400	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr12:9180400-9183400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr12:9180600-9184200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:9180600-9185000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:9181400-9184400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:9181400-9184800	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr12:9182200-9185000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr12:9182600-9184000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr12:9182800-9183400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:9182800-9186600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:9183000-9183600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:9183000-9186400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr12:9183000-9186600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr12:9183200-9183800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr12:9183200-9184000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr12:9183200-9184400	Enhancers	Primary T cells from cord blood	blood
21	chr12:9183400-9183600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:9183400-9183600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:9183400-9183800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr12:9183400-9183800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr12:9183400-9183800	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr12:9183400-9183800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr12:9183400-9184000	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr12:9183400-9184200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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