Variant report

Variant	rs462878
Chromosome Location	chr2:32438655-32438656
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11678119	0.82[CEU][hapmap]
rs11691939	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs12478134	1.00[CEU][hapmap]
rs12614686	0.82[CEU][hapmap]
rs12991444	0.87[CEU][hapmap];0.95[GIH][hapmap];0.90[TSI][hapmap]
rs12996943	0.82[EUR][1000 genomes]
rs13006495	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs13006880	0.82[EUR][1000 genomes]
rs13013695	0.93[GIH][hapmap];0.83[TSI][hapmap]
rs17011801	1.00[CEU][hapmap]
rs177082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs186135	0.81[EUR][1000 genomes]
rs212682	0.88[EUR][1000 genomes]
rs212684	0.92[EUR][1000 genomes]
rs212689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212690	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212696	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs212702	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs212710	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs212736	0.93[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs212751	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs212754	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs212761	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs2280968	1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs2294178	0.85[EUR][1000 genomes]
rs2366547	0.86[CEU][hapmap]
rs34197800	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs34835885	0.81[EUR][1000 genomes]
rs35978916	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs375050	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3752916	0.82[CEU][hapmap]
rs3769602	0.82[CEU][hapmap]
rs3769605	0.93[CEU][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap]
rs3851310	0.82[CEU][hapmap]
rs410469	0.93[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs56322034	0.87[EUR][1000 genomes]
rs6543648	0.81[EUR][1000 genomes]
rs6723154	0.82[CEU][hapmap]
rs6756085	0.84[EUR][1000 genomes]
rs686005	0.82[EUR][1000 genomes]
rs7562653	0.93[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs7572964	0.82[CEU][hapmap]
rs7574000	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs805831	0.83[EUR][1000 genomes]
rs9789593	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2422335	chr2:32412330-33200581	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs462878	SLC30A6	cis	parietal	SCAN
rs462878	SLC30A6	cis	cerebellum	SCAN
rs462878	EHD3	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32391600-32452800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:32391800-32453800	Weak transcription	Colonic Mucosa	Colon
3	chr2:32392200-32445200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:32392800-32447600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:32399200-32449600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:32403000-32452200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:32404200-32445200	Weak transcription	Brain Angular Gyrus	brain
8	chr2:32404200-32447600	Weak transcription	Pancreas	Pancrea
9	chr2:32404200-32448000	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:32404200-32452400	Weak transcription	Right Ventricle	heart
11	chr2:32404200-32460600	Weak transcription	Esophagus	oesophagus
12	chr2:32404400-32447400	Weak transcription	HUVEC	blood vessel
13	chr2:32404400-32450800	Weak transcription	Gastric	stomach
14	chr2:32404800-32447800	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:32410400-32445200	Weak transcription	Fetal Kidney	kidney
16	chr2:32410600-32445200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr2:32411400-32445400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:32411600-32447800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:32412000-32450400	Weak transcription	Spleen	Spleen
20	chr2:32412200-32444200	Weak transcription	Fetal Brain Female	brain
21	chr2:32412800-32445200	Weak transcription	Brain Substantia Nigra	brain
22	chr2:32415200-32445200	Weak transcription	HMEC	breast
23	chr2:32419200-32446800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:32419800-32445200	Weak transcription	HSMM	muscle
25	chr2:32420800-32447000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:32421200-32445000	Weak transcription	Thymus	Thymus
27	chr2:32421200-32445400	Weak transcription	Fetal Heart	heart
28	chr2:32421400-32443000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:32422000-32452400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:32423000-32443200	Weak transcription	GM12878-XiMat	blood
31	chr2:32423000-32447400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:32423400-32448000	Weak transcription	Small Intestine	intestine
33	chr2:32423600-32445200	Weak transcription	NH-A	brain
34	chr2:32424400-32445200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:32424400-32447400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:32424400-32447600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:32424400-32447600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:32424400-32455400	Weak transcription	Fetal Brain Male	brain
39	chr2:32426400-32455000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:32426800-32443000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:32426800-32443200	Weak transcription	NHEK	skin
42	chr2:32426800-32445000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:32426800-32445200	Weak transcription	HSMMtube	muscle
44	chr2:32426800-32447600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:32426800-32447600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:32427000-32444400	Weak transcription	Lung	lung
47	chr2:32427000-32444800	Weak transcription	Dnd41	blood
48	chr2:32427000-32447400	Weak transcription	Ovary	ovary
49	chr2:32427200-32445200	Weak transcription	A549	lung
50	chr2:32427400-32444400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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