Variant report

Variant	rs3026252
Chromosome Location	chr12:9160234-9160235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9100812..9102729-chr12:9160116..9162568,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139187	Chromatin interaction
ENSG00000003056	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11048494	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11048496	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11502446	0.94[ASN][1000 genomes]
rs12303154	0.82[EUR][1000 genomes]
rs12322917	0.82[EUR][1000 genomes]
rs12423652	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12809367	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12811795	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12812329	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12816157	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12819409	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12819575	0.92[CEU][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12822685	0.95[CEU][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12826054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12826978	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12827501	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12828013	0.91[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17730391	0.92[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1805668	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1805669	0.82[EUR][1000 genomes]
rs1805670	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805671	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805672	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805707	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1805716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159959	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2159960	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2377678	0.82[EUR][1000 genomes]
rs2377679	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2377680	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3026244	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3026251	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34236568	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34365749	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34533518	0.82[EUR][1000 genomes]
rs34651717	0.82[EUR][1000 genomes]
rs34722215	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34920912	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35176717	0.82[EUR][1000 genomes]
rs35377225	0.82[EUR][1000 genomes]
rs35557651	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35596029	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35882740	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36061702	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3741854	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883208	0.82[EUR][1000 genomes]
rs4883209	0.82[EUR][1000 genomes]
rs56083774	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56143043	0.82[EUR][1000 genomes]
rs56350793	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60267183	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61915986	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61916006	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7136274	0.82[EUR][1000 genomes]
rs7136774	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7302472	0.99[ASN][1000 genomes]
rs7311267	0.81[CEU][hapmap]
rs7311509	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs759468	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs759469	0.82[EUR][1000 genomes]
rs759470	0.82[EUR][1000 genomes]
rs7953214	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3026252	KLRG1	cis	multi-tissue	Pritchard

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9133800-9164600	Weak transcription	Psoas Muscle	Psoas
2	chr12:9133800-9170200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr12:9142400-9168000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr12:9146400-9161200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:9149600-9161000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:9150000-9160800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:9150000-9161000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr12:9150000-9162000	Weak transcription	Adipose Nuclei	Adipose
9	chr12:9150000-9164000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:9152400-9167600	Weak transcription	Left Ventricle	heart
11	chr12:9154400-9160800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:9154400-9161200	Weak transcription	Primary T cells from cord blood	blood
13	chr12:9154400-9161200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:9155600-9160800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:9155600-9161000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr12:9155800-9160600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:9155800-9160800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:9155800-9161200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:9158200-9161200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:9158800-9160800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr12:9159600-9168400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr12:9159800-9160400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:9159800-9160800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:9160200-9161000	Strong transcription	Primary T cells fromperipheralblood	blood

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