Variant report

Variant	rs12423652
Chromosome Location	chr12:9177033-9177034
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9064573..9067189-chr12:9176082..9178403,2	K562	blood:
2	chr12:9101626..9103314-chr12:9176948..9179841,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111752	Chromatin interaction
ENSG00000003056	Chromatin interaction
ENSG00000139187	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11048494	0.81[EUR][1000 genomes]
rs11048496	0.81[EUR][1000 genomes]
rs12303154	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12322917	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12809367	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12811795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812329	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12816157	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12819409	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12819575	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12822685	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12826054	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12826978	0.80[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12827501	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12828013	0.90[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17730331	0.96[ASN][1000 genomes]
rs17730391	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1805668	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1805669	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1805670	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1805671	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1805672	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1805673	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1805674	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1805675	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1805676	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1805707	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1805716	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2159959	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2159960	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2377678	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2377679	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2377680	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2889705	0.99[ASN][1000 genomes]
rs3026243	0.96[ASN][1000 genomes]
rs3026244	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3026251	0.80[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3026252	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34236568	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34365749	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34533518	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34651717	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34722215	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34920912	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35176717	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35377225	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35557651	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35596029	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35882740	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36061702	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3741854	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4883206	0.99[ASN][1000 genomes]
rs4883208	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4883209	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56083774	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56143043	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56350793	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60267183	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61915986	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61916006	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136274	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136774	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7311267	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7311509	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs759468	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs759469	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs759470	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7957626	0.95[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	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
3	esv2754892	chr12:9136351-9179007	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv973020	chr12:9163929-9182709	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12423652	KLRG1	cis	multi-tissue	Pritchard

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9165800-9182400	Weak transcription	Adipose Nuclei	Adipose
2	chr12:9174400-9177200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr12:9174400-9181800	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr12:9174600-9177200	Enhancers	Primary T cells fromperipheralblood	blood
5	chr12:9174600-9177400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:9174800-9177200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr12:9174800-9177200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:9174800-9177200	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr12:9174800-9185800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:9175200-9177200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:9175200-9185800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr12:9175400-9177200	Enhancers	Fetal Thymus	thymus
13	chr12:9175800-9177400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:9176000-9178200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr12:9176600-9182800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:9177000-9177400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:9177000-9177600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr12:9177000-9178400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:9177000-9178600	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr12:9177000-9179000	Enhancers	Thymus	Thymus
21	chr12:9177000-9180600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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