Variant report

Variant	rs10842662
Chromosome Location	chr12:9139344-9139345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs1049925	0.81[AMR][1000 genomes]
rs10842660	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842696	0.87[ASN][1000 genomes]
rs11048190	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11048195	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11048264	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11048337	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11048338	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11048344	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11048345	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11048434	0.89[ASN][1000 genomes]
rs11494569	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11494570	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12371786	0.83[AMR][1000 genomes]
rs12422905	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12423746	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12423817	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12424026	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12812913	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12816518	0.89[ASN][1000 genomes]
rs12817960	0.89[ASN][1000 genomes]
rs12820395	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821842	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12823100	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12824140	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12824212	0.89[ASN][1000 genomes]
rs12824380	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12827055	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12827988	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12828902	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12833375	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1476911	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1805677	0.89[ASN][1000 genomes]
rs1805719	0.90[ASN][1000 genomes]
rs1805721	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1805722	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805723	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805724	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1805732	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1805733	0.82[AMR][1000 genomes]
rs1805736	0.81[AMR][1000 genomes]
rs1805761	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1805765	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2041624	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2041625	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2080116	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080117	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110190	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2110191	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2110192	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2268021	0.89[ASN][1000 genomes]
rs2377672	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2377673	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2377674	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34285491	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34798934	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35870866	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4254119	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4309200	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7300767	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7301381	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7302417	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7309922	0.81[AMR][1000 genomes]
rs7314942	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7315055	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7957321	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7971932	0.87[ASN][1000 genomes]
rs933462	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[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	nsv819596	chr12:9113514-9141537	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	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
rs10842662	KLRG1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9133200-9139800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:9133600-9140600	Weak transcription	Spleen	Spleen
3	chr12:9133800-9164600	Weak transcription	Psoas Muscle	Psoas
4	chr12:9133800-9170200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr12:9135800-9141800	Weak transcription	Primary B cells from cord blood	blood
6	chr12:9137600-9139800	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr12:9137600-9139800	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr12:9137600-9142000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr12:9137800-9141800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr12:9137800-9141800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:9137800-9142200	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr12:9138000-9140200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:9138000-9142200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr12:9138000-9143000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr12:9138400-9139800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr12:9138400-9140200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:9138400-9140200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr12:9138400-9142200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:9138600-9142200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:9139000-9142200	Enhancers	Primary T cells from cord blood	blood
21	chr12:9139200-9139600	Enhancers	Fetal Thymus	thymus
22	chr12:9139200-9140000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:9139200-9142200	Enhancers	Primary hematopoietic stem cells	blood
24	chr12:9139200-9142200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:9139200-9144400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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