Variant report

Variant	rs2130413
Chromosome Location	chr8:48482098-48482099
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10094128	0.82[CEU][hapmap]
rs10957549	0.96[EUR][1000 genomes]
rs10957644	0.96[EUR][1000 genomes]
rs10958058	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1106607	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11778548	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11782572	0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11784823	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12544329	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs12549996	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12675378	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12678110	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs16926260	1.00[YRI][hapmap]
rs16928696	0.98[EUR][1000 genomes]
rs1872840	0.89[EUR][1000 genomes]
rs2129617	0.96[CEU][hapmap];0.87[CHD][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2129618	0.92[EUR][1000 genomes]
rs2130412	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2171854	1.00[YRI][hapmap]
rs2362554	0.94[JPT][hapmap];1.00[YRI][hapmap]
rs4489323	0.87[EUR][1000 genomes]
rs4536257	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4594029	0.82[CEU][hapmap]
rs4608108	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs4873102	1.00[ASW][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap]
rs4873106	1.00[ASW][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs4873368	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4873395	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs4873399	0.94[EUR][1000 genomes]
rs4873437	0.98[EUR][1000 genomes]
rs4873477	1.00[YRI][hapmap]
rs4873478	0.82[CEU][hapmap]
rs4873507	0.89[EUR][1000 genomes]
rs4873529	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4873546	0.81[CEU][hapmap]
rs4873565	0.92[EUR][1000 genomes]
rs4873619	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs55941013	0.95[EUR][1000 genomes]
rs56092229	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62539116	0.94[EUR][1000 genomes]
rs62539144	0.91[EUR][1000 genomes]
rs62539147	0.91[EUR][1000 genomes]
rs62539150	0.89[EUR][1000 genomes]
rs6982620	1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs6986054	0.82[CEU][hapmap]
rs6987043	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs6989917	0.98[EUR][1000 genomes]
rs7002441	1.00[YRI][hapmap]
rs7842068	0.82[CEU][hapmap]
rs876915	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs923499	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[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	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1025674	chr8:48306843-48548862	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv890848	chr8:48405007-48535622	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv470211	chr8:48405007-48545961	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1027043	chr8:48444306-48637900	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv539596	chr8:48444306-48637900	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1029297	chr8:48468835-48530803	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1030163	chr8:48468835-48544495	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2130413	KIAA0146	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48466800-48522600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:48467400-48482400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr8:48467400-48484600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:48467400-48485400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr8:48467400-48485800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr8:48467400-48486000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr8:48467400-48486000	Weak transcription	Esophagus	oesophagus
8	chr8:48467400-48486000	Weak transcription	Gastric	stomach
9	chr8:48467400-48486000	Weak transcription	Ovary	ovary
10	chr8:48467400-48492400	Weak transcription	Left Ventricle	heart
11	chr8:48473000-48511400	Weak transcription	Primary T cells from cord blood	blood
12	chr8:48473600-48485400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr8:48475200-48483000	Weak transcription	Placenta	Placenta
14	chr8:48475400-48482800	Weak transcription	Fetal Lung	lung
15	chr8:48475800-48485800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr8:48476000-48486200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr8:48479400-48496200	Weak transcription	Fetal Intestine Small	intestine
18	chr8:48479600-48486000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr8:48479600-48486200	Weak transcription	HSMMtube	muscle
20	chr8:48480400-48485400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr8:48480400-48503000	Weak transcription	Primary B cells from cord blood	blood
22	chr8:48481000-48503200	Weak transcription	Dnd41	blood
23	chr8:48481200-48485400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr8:48481200-48513600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr8:48481400-48487200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr8:48481400-48494600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr8:48481600-48485600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr8:48482000-48492200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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