Variant report

Variant	rs10992461
Chromosome Location	chr9:95536802-95536803
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95524574..95529988-chr9:95531032..95538459,18	K562	blood:
2	chr9:95526215..95528436-chr9:95535062..95537228,2	MCF-7	breast:
3	chr9:95532566..95534480-chr9:95535486..95538375,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185963	Chromatin interaction

Extended variants
information (count: 165 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:164)

rs_ID	r²[population]
rs1010823	0.85[ASN][1000 genomes]
rs1040977	0.82[EUR][1000 genomes]
rs10820997	0.84[MEX][hapmap]
rs10820998	0.84[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10821001	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821002	0.82[ASN][1000 genomes]
rs10821003	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821004	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821005	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821007	0.84[ASN][1000 genomes]
rs10821009	0.88[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs10821010	0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs10821011	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821012	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs10821014	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821015	0.85[ASN][1000 genomes]
rs10821016	0.85[ASN][1000 genomes]
rs10992380	0.82[CHB][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs10992382	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs10992384	0.84[CEU][hapmap];0.88[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs10992390	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[EUR][1000 genomes]
rs10992392	0.84[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs10992396	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10992404	0.85[ASN][1000 genomes]
rs10992406	0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992407	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992408	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10992409	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10992412	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992413	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs10992414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992416	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992417	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992418	0.82[ASN][1000 genomes]
rs10992419	0.82[ASN][1000 genomes]
rs10992420	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992422	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992423	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992426	0.93[ASN][1000 genomes]
rs10992427	0.82[ASN][1000 genomes]
rs10992430	0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs10992431	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs10992432	0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs10992433	0.94[ASN][1000 genomes]
rs10992434	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs10992436	0.81[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992437	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992438	0.85[ASN][1000 genomes]
rs10992441	0.85[ASN][1000 genomes]
rs10992442	0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992443	0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992444	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs10992445	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs10992447	1.00[CEU][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs10992448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992451	0.81[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992456	0.85[ASN][1000 genomes]
rs10992460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992462	0.85[ASN][1000 genomes]
rs10992469	0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992474	0.88[EUR][1000 genomes]
rs10992476	0.90[EUR][1000 genomes]
rs1117670	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs1125063	0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs1125064	0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs11533010	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11535540	0.82[ASN][1000 genomes]
rs12057034	0.89[EUR][1000 genomes]
rs12236013	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12236393	0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12236516	0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs12236747	0.85[ASN][1000 genomes]
rs12236754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236788	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12237216	0.83[ASN][1000 genomes]
rs12238691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12683944	0.85[ASN][1000 genomes]
rs12684076	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12684587	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12685256	0.82[ASN][1000 genomes]
rs12685257	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs12685358	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12685780	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs12685791	0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs12686058	0.84[ASN][1000 genomes]
rs12686771	1.00[CEU][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs1323523	0.84[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes]
rs1326775	0.84[CEU][hapmap];0.88[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs1407944	0.96[ASN][1000 genomes]
rs1552908	0.84[MEX][hapmap]
rs1555574	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1575460	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs16908555	0.92[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs16908560	0.91[CEU][hapmap];0.89[GIH][hapmap];0.89[EUR][1000 genomes]
rs17366488	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1853428	0.92[CEU][hapmap]
rs1853429	0.89[EUR][1000 genomes]
rs1853468	0.84[CEU][hapmap];0.88[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs1974004	0.92[CEU][hapmap]
rs1980705	0.84[MEX][hapmap]
rs2038685	0.81[AMR][1000 genomes]
rs2146848	0.84[CEU][hapmap]
rs2148537	0.84[CEU][hapmap];0.88[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs2181584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2181586	0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2277164	0.89[ASN][1000 genomes]
rs2281888	0.84[MEX][hapmap]
rs2296080	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs2398780	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs3203916	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs3739605	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];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4141966	0.89[EUR][1000 genomes]
rs4545157	0.85[ASN][1000 genomes]
rs556	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs56111209	0.85[ASN][1000 genomes]
rs56203846	0.82[ASN][1000 genomes]
rs56311406	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56339669	0.84[ASN][1000 genomes]
rs57421019	0.85[ASN][1000 genomes]
rs57720404	0.85[ASN][1000 genomes]
rs57737182	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58952648	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60173654	0.85[ASN][1000 genomes]
rs60457563	0.85[ASN][1000 genomes]
rs60498616	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6479426	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs67601697	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs68022962	0.85[ASN][1000 genomes]
rs68046436	0.85[ASN][1000 genomes]
rs7031163	0.86[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];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037961	0.82[ASN][1000 genomes]
rs753802	0.81[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs753803	0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs753804	0.84[CEU][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754600	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7850075	0.92[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7850871	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7851947	0.96[ASN][1000 genomes]
rs7853617	0.84[EUR][1000 genomes]
rs7855203	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7856147	0.84[CEU][hapmap];0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7857105	0.84[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs7857502	0.84[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7859967	0.86[EUR][1000 genomes]
rs7860628	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7862106	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7863741	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7863882	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs7863890	0.84[MEX][hapmap]
rs7869529	0.82[ASN][1000 genomes]
rs7869603	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7871537	0.84[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7875050	0.90[CEU][hapmap];0.94[CHB][hapmap];0.85[EUR][1000 genomes]
rs7875225	0.83[JPT][hapmap]
rs8181065	0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs878610	0.85[ASN][1000 genomes]
rs879812	0.84[MEX][hapmap]
rs912259	0.85[ASN][1000 genomes]
rs912261	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs912264	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs971984	0.84[CEU][hapmap];0.88[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes]
rs976320	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs976321	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430081	chr9:95502571-95568110	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10992461	OMD	cis	parietal	SCAN
rs10992461	ANKRD19	cis	cerebellum	SCAN
rs10992461	CENPP	cis	multi-tissue	Pritchard
rs10992461	FBP1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95533200-95537600	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr9:95533200-95541200	Weak transcription	Left Ventricle	heart
3	chr9:95533400-95541200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:95533400-95543200	Weak transcription	Esophagus	oesophagus
5	chr9:95533600-95537800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr9:95533800-95537400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:95533800-95537800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:95534000-95537600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr9:95534000-95537800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr9:95536000-95537600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:95536200-95537000	Enhancers	NHLF	lung
12	chr9:95536200-95537200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:95536200-95537200	Enhancers	NH-A	brain
14	chr9:95536200-95537200	Enhancers	NHDF-Ad	bronchial
15	chr9:95536200-95537400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:95536200-95537600	Enhancers	HMEC	breast
17	chr9:95536200-95537600	Enhancers	NHEK	skin
18	chr9:95536200-95538200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:95536400-95537200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:95536400-95537200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:95536400-95537200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:95536400-95537200	Enhancers	HSMM	muscle
23	chr9:95536400-95537200	Enhancers	Osteobl	bone
24	chr9:95536400-95537400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:95536400-95537600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr9:95536600-95537000	Weak transcription	Primary B cells from cord blood	blood
27	chr9:95536600-95537000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:95536600-95537000	Enhancers	Brain Hippocampus Middle	brain
29	chr9:95536600-95537000	Enhancers	Fetal Brain Female	brain
30	chr9:95536600-95537400	Enhancers	Brain Anterior Caudate	brain
31	chr9:95536600-95537800	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr9:95536600-95539000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr9:95536800-95537400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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