Variant report

Variant	rs10992406
Chromosome Location	chr9:95443071-95443072
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr9:95442185-95443776	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr9:95442194-95443153	U87	brain:	n/a	n/a
3	POLR2A	chr9:95442194-95443159	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95436301..95439240-chr9:95442495..95445475,2	K562	blood:
2	chr9:95432210..95434644-chr9:95442225..95447391,5	K562	blood:
3	chr9:95440290..95443133-chr9:95467727..95470329,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213669	TF binding region
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 159 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs1010823	0.80[EUR][1000 genomes]
rs10491806	0.89[CHB][hapmap]
rs10820997	0.86[JPT][hapmap]
rs10820998	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10821000	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10821001	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10821002	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10821003	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10821004	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10821005	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10821007	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10821009	0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10821010	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10821011	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10821012	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10821014	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10821015	0.80[EUR][1000 genomes]
rs10821016	0.80[EUR][1000 genomes]
rs10821017	0.88[EUR][1000 genomes]
rs10992367	0.88[CHB][hapmap]
rs10992380	0.88[CHB][hapmap]
rs10992382	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10992384	0.94[CHB][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs10992390	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10992392	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10992394	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992396	0.99[ASN][1000 genomes]
rs10992402	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10992403	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10992404	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992407	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10992408	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10992409	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10992412	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10992413	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10992414	0.92[CEU][hapmap];0.94[CHB][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10992416	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10992417	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10992419	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10992420	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10992422	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10992423	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10992426	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992427	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992430	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992431	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992432	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992433	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10992434	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992436	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992437	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10992438	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992441	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992442	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992443	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992444	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992445	0.82[AMR][1000 genomes]
rs10992447	0.91[CEU][hapmap]
rs10992448	0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs10992451	0.80[EUR][1000 genomes]
rs10992453	0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992456	0.80[EUR][1000 genomes]
rs10992460	0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992461	0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992475	0.83[EUR][1000 genomes]
rs1117670	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1125063	0.80[EUR][1000 genomes]
rs1125064	0.80[EUR][1000 genomes]
rs11533010	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12236013	0.88[ASN][1000 genomes]
rs12236393	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12236516	0.80[EUR][1000 genomes]
rs12236747	0.80[EUR][1000 genomes]
rs12236754	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs12236788	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12237216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12238691	0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12683944	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12684587	0.84[ASN][1000 genomes]
rs12685080	0.83[CHB][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs12685256	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12685257	0.80[EUR][1000 genomes]
rs12685358	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12685780	0.80[EUR][1000 genomes]
rs12685791	0.80[EUR][1000 genomes]
rs12686058	0.80[EUR][1000 genomes]
rs12686771	0.91[CEU][hapmap]
rs12686780	0.81[AFR][1000 genomes]
rs12686781	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs1323523	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs1326775	0.94[CHB][hapmap];0.93[YRI][hapmap]
rs1407944	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1575460	0.94[CHB][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs16908555	0.83[CEU][hapmap]
rs16908560	0.84[CEU][hapmap]
rs17366488	0.90[ASN][1000 genomes]
rs1853427	0.83[EUR][1000 genomes]
rs1853428	0.83[CEU][hapmap]
rs1853468	0.94[CHB][hapmap]
rs1874128	0.87[YRI][hapmap]
rs1974004	0.83[CEU][hapmap]
rs1980705	0.81[YRI][hapmap]
rs2088055	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2131919	0.88[CHB][hapmap]
rs2148537	0.94[CHB][hapmap];0.93[YRI][hapmap]
rs2181584	0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2181586	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2274413	0.83[YRI][hapmap]
rs2277164	0.85[EUR][1000 genomes]
rs2277166	0.81[AMR][1000 genomes]
rs2281888	0.81[YRI][hapmap]
rs2296080	0.82[AMR][1000 genomes]
rs3203916	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3739605	0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs41266683	0.82[AMR][1000 genomes]
rs556	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56203846	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56311406	0.85[ASN][1000 genomes]
rs56339669	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs57720404	0.80[EUR][1000 genomes]
rs57737182	0.85[ASN][1000 genomes]
rs58952648	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs60173654	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60498616	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6479426	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66493272	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67601697	0.88[ASN][1000 genomes]
rs68046436	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7031163	0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs7037961	0.82[AMR][1000 genomes]
rs72618187	0.83[EUR][1000 genomes]
rs753802	0.82[AMR][1000 genomes]
rs753803	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs753804	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs754600	0.92[ASN][1000 genomes]
rs7850075	0.83[CEU][hapmap]
rs7850871	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7851947	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7853617	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7856147	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7857105	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7857502	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7860628	0.82[ASN][1000 genomes]
rs7863882	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7863890	0.86[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes]
rs7864889	0.86[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes]
rs7869529	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7869603	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7875050	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7875227	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8181065	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs878610	0.80[EUR][1000 genomes]
rs879812	0.86[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes]
rs912259	0.80[AMR][1000 genomes]
rs912261	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];0.99[ASN][1000 genomes]
rs912264	0.82[CHB][hapmap]
rs971984	0.94[CHB][hapmap]
rs976320	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9775970	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10992406	CENPP	cis	multi-tissue	Pritchard
rs10992406	BICD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95433800-95444000	Weak transcription	Fetal Brain Female	brain
2	chr9:95441800-95443200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:95441800-95443200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:95441800-95444200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:95441800-95444400	Enhancers	HMEC	breast
6	chr9:95442200-95443200	Enhancers	HSMM	muscle
7	chr9:95442200-95443400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:95442200-95443400	Enhancers	Osteobl	bone
9	chr9:95442200-95443600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:95442400-95443200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:95442400-95443200	Enhancers	NHDF-Ad	bronchial
12	chr9:95442400-95443400	Enhancers	Esophagus	oesophagus
13	chr9:95442400-95443600	Flanking Active TSS	NHEK	skin
14	chr9:95442600-95443200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:95442600-95443200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:95442600-95443200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:95442800-95443200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:95443000-95443200	Enhancers	Placenta Amnion	Placenta Amnion
19	chr9:95443000-95443600	Weak transcription	Spleen	Spleen

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