Variant report

Variant	rs10458088
Chromosome Location	chr6:5528882-5528883
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10900969	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10900970	1.00[ASW][hapmap];0.91[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11243014	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11243017	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11758395	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12175572	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12527880	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935992	0.91[CEU][hapmap];0.88[CHB][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7746396	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7763423	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs9328309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9378957	0.81[ASN][1000 genomes]
rs9378958	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs9378959	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9378960	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9378962	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9392690	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9392691	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9405272	0.83[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs9405273	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs9405274	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9405842	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs9405843	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1023027	chr6:5377308-5556749	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538121	chr6:5377308-5556749	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1017506	chr6:5443538-5551125	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv883420	chr6:5524393-5584422	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10458088	FAM150B	trans	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5501000-5550600	Weak transcription	Pancreas	Pancrea
2	chr6:5508000-5547400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:5511200-5546400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:5511400-5540200	Weak transcription	Esophagus	oesophagus
5	chr6:5511400-5568200	Weak transcription	Aorta	Aorta
6	chr6:5514000-5537400	Weak transcription	Left Ventricle	heart
7	chr6:5518600-5550000	Weak transcription	Right Ventricle	heart
8	chr6:5522600-5531400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:5522600-5544600	Weak transcription	Ovary	ovary
10	chr6:5522600-5548000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:5522800-5550400	Weak transcription	GM12878-XiMat	blood
12	chr6:5523000-5549000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:5523400-5531200	Weak transcription	Primary T cells from cord blood	blood
14	chr6:5523600-5531400	Weak transcription	Fetal Thymus	thymus
15	chr6:5525200-5530000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:5525200-5547600	Weak transcription	Primary B cells from cord blood	blood
17	chr6:5525400-5529000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:5525400-5531400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:5525800-5530000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:5525800-5531400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:5526200-5531400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr6:5526400-5530000	Weak transcription	NHDF-Ad	bronchial
23	chr6:5528000-5529400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:5528400-5529000	Enhancers	Primary B cells from peripheral blood	blood
25	chr6:5528600-5529800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:5528800-5529000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:5528800-5529000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr6:5528800-5529400	Enhancers	H9 Cell Line	embryonic stem cell

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