Variant report

Variant	rs1805673
Chromosome Location	chr12:9163059-9163060
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	chr12:9157659..9159439-chr12:9161450..9164436,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11048434	0.84[ASW][hapmap];0.83[CHD][hapmap]
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[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12809367	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12811795	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12812329	0.80[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	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12819575	0.92[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12822685	0.95[CEU][hapmap];0.81[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12824212	0.83[CHD][hapmap]
rs12826054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12826978	1.00[CHB][hapmap];1.00[JPT][hapmap];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	0.90[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17730391	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];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	0.80[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[ASW][hapmap];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805677	0.84[ASW][hapmap];0.85[CHD][hapmap]
rs1805707	0.84[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs1805716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159959	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2159960	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2377678	0.82[EUR][1000 genomes]
rs2377679	0.87[CEU][hapmap];0.81[JPT][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];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3026252	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]
rs34236568	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34365749	0.80[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	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34920912	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	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35882740	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36061702	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3741854	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	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56143043	0.82[EUR][1000 genomes]
rs56350793	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60267183	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61915986	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61916006	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7136274	0.82[EUR][1000 genomes]
rs7136774	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7302472	0.99[ASN][1000 genomes]
rs7311267	0.81[CEU][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap]
rs7311509	0.88[CEU][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.82[EUR][1000 genomes]
rs759468	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1805673	KLRG1	cis	cerebellum	SCAN
rs1805673	KLRG1	cis	multi-tissue	Pritchard
rs1805673	CLEC6A	cis	cerebellum	SCAN
rs1805673	APOLD1	cis	parietal	SCAN
rs1805673	CSDA	cis	cerebellum	SCAN

Chromatin state (count:28 , 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	chr12:9150000-9164000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:9152400-9167600	Weak transcription	Left Ventricle	heart
6	chr12:9159600-9168400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr12:9160800-9164800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:9160800-9165400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:9161000-9164200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:9161000-9165600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:9161000-9166200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr12:9161000-9166400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:9161200-9165600	Genic enhancers	Primary T cells fromperipheralblood	blood
14	chr12:9161400-9163800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr12:9161400-9164400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:9161400-9166200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:9161400-9166400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:9161600-9164800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
19	chr12:9162000-9165800	Strong transcription	Adipose Nuclei	Adipose
20	chr12:9162000-9166200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr12:9162200-9164200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:9162200-9164200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:9162200-9165800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr12:9162600-9164600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr12:9162600-9167200	Weak transcription	Brain Anterior Caudate	brain
26	chr12:9162800-9163400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:9162800-9163600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:9163000-9163600	Weak transcription	Primary T cells from cord blood	blood

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