Variant report

Variant	rs10882019
Chromosome Location	chr10:93815988-93815989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10509640	0.84[JPT][hapmap]
rs10786026	0.88[JPT][hapmap]
rs10882034	0.84[LWK][hapmap]
rs1104012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs11186825	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11186828	0.86[ASN][1000 genomes]
rs11186851	0.80[MKK][hapmap]
rs11186872	0.84[LWK][hapmap];0.85[MKK][hapmap]
rs11817194	0.84[JPT][hapmap]
rs11818152	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12254369	0.84[JPT][hapmap]
rs12256118	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12263532	0.93[JPT][hapmap]
rs1229580	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17107472	1.00[JPT][hapmap]
rs1711850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1935864	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2048901	0.84[JPT][hapmap]
rs2252200	0.83[GIH][hapmap];0.84[JPT][hapmap]
rs2676824	0.81[GIH][hapmap];0.84[JPT][hapmap]
rs2792019	0.84[JPT][hapmap]
rs2797645	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4486531	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4509678	0.84[JPT][hapmap]
rs4642987	0.83[GIH][hapmap];0.84[JPT][hapmap]
rs55901992	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6583801	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[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7070076	0.83[GIH][hapmap];0.84[JPT][hapmap]
rs7077333	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7093436	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7093730	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73314327	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7909870	0.84[JPT][hapmap]
rs7911552	0.82[GIH][hapmap];0.84[JPT][hapmap]
rs7912721	0.88[JPT][hapmap]
rs7916626	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7917088	0.82[MKK][hapmap]
rs833364	0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs833365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs833368	0.83[GIH][hapmap];0.84[JPT][hapmap]
rs833380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833386	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9787645	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051226	chr10:93711296-93915586	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv540745	chr10:93711296-93915586	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1042818	chr10:93715483-93855032	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv895893	chr10:93747260-93875264	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv551923	chr10:93804974-93835969	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10882019	BTAF1	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93787400-93818400	Weak transcription	Colonic Mucosa	Colon
2	chr10:93787400-93840000	Weak transcription	Small Intestine	intestine
3	chr10:93787600-93828000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr10:93789800-93816400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr10:93791800-93838400	Weak transcription	Brain Substantia Nigra	brain
6	chr10:93792800-93837800	Weak transcription	Brain Angular Gyrus	brain
7	chr10:93794400-93837200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr10:93795800-93824200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:93796200-93840800	Weak transcription	Psoas Muscle	Psoas
10	chr10:93799200-93824000	Weak transcription	HSMMtube	muscle
11	chr10:93805600-93817200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr10:93806000-93817600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr10:93806000-93819400	Weak transcription	Brain Germinal Matrix	brain
14	chr10:93808000-93816600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr10:93808000-93817000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr10:93808000-93820000	Weak transcription	Fetal Brain Female	brain
17	chr10:93808000-93825400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr10:93808000-93825600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:93808000-93842600	Weak transcription	Fetal Lung	lung
20	chr10:93808200-93817200	Weak transcription	Esophagus	oesophagus
21	chr10:93808200-93842800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr10:93808400-93825400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr10:93808400-93834400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr10:93808400-93844400	Weak transcription	Primary T cells from cord blood	blood
25	chr10:93810000-93817800	Strong transcription	Liver	Liver
26	chr10:93812200-93816800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr10:93812200-93835800	Weak transcription	Aorta	Aorta
28	chr10:93812400-93837800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr10:93812800-93816200	Weak transcription	Lung	lung
30	chr10:93812800-93816800	Weak transcription	Brain Anterior Caudate	brain
31	chr10:93812800-93834600	Weak transcription	Adipose Nuclei	Adipose
32	chr10:93812800-93834800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr10:93812800-93837200	Weak transcription	Ovary	ovary
34	chr10:93812800-93837800	Weak transcription	Brain Hippocampus Middle	brain
35	chr10:93812800-93837800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr10:93812800-93838200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr10:93812800-93838800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr10:93812800-93839800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr10:93812800-93840600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr10:93814000-93817600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr10:93814600-93817200	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr10:93814600-93817400	Strong transcription	Brain Cingulate Gyrus	brain
43	chr10:93814600-93817600	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr10:93814800-93816800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr10:93815000-93834600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr10:93815200-93816000	Strong transcription	Left Ventricle	heart
47	chr10:93815200-93816400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr10:93815400-93838200	Weak transcription	Primary B cells from cord blood	blood
49	chr10:93815400-93847200	Weak transcription	Hela-S3	cervix
50	chr10:93815600-93817000	Strong transcription	Pancreas	Pancrea

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