Variant report

Variant	rs7976808
Chromosome Location	chr12:9206029-9206030
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10743598	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10771307	0.86[CHD][hapmap]
rs10771308	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10771309	0.86[CHD][hapmap]
rs10842789	0.93[CHD][hapmap]
rs10842839	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10842849	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11048789	0.86[CHD][hapmap]
rs11048839	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs113973	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.86[LWK][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1805651	0.86[CHD][hapmap]
rs1805663	0.86[CHD][hapmap]
rs1805666	0.82[CHB][hapmap]
rs1805682	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2193006	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2216143	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226379	0.86[CHD][hapmap]
rs226380	0.92[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226381	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226382	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs226386	0.92[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226387	0.92[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs226388	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226389	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226390	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226391	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226392	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226394	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226400	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs226401	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs226403	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs226408	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs226415	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3759277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4882977	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487584	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs669	0.93[CHD][hapmap]
rs71453666	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7295733	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955940	0.86[CHD][hapmap]
rs7964085	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965790	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs881376	0.86[CHD][hapmap]

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	nsv898738	chr12:9205030-9274394	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7976808	CLEC1A	cis	cerebellum	SCAN
rs7976808	ZNF705A	cis	cerebellum	SCAN
rs7976808	CLEC1B	cis	parietal	SCAN
rs7976808	GAPDH	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9178400-9216400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:9199600-9207000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:9199600-9216200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:9199800-9216200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:9199800-9216200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:9199800-9216600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:9200000-9216000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:9200000-9216200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:9200000-9216200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:9200000-9216200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:9202000-9216600	Weak transcription	Left Ventricle	heart
12	chr12:9202200-9207400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:9202200-9216200	Weak transcription	Primary T cells from cord blood	blood
14	chr12:9202200-9216200	Weak transcription	Adipose Nuclei	Adipose
15	chr12:9202400-9216000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:9204200-9216800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:9205000-9208000	Weak transcription	Primary T cells fromperipheralblood	blood

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