Variant report

Variant	rs12236788
Chromosome Location	chr9:95542654-95542655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95527312..95529710-chr9:95541794..95545254,3	K562	blood:
2	chr9:95533275..95536174-chr9:95541211..95543902,2	MCF-7	breast:
3	chr9:95540552..95544510-chr9:95545450..95549411,3	K562	blood:

Extended variants
information (count: 157 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:156)

rs_ID	r²[population]
rs1010823	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10820997	0.84[MEX][hapmap]
rs10820998	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[MEX][hapmap]
rs10821001	0.94[ASN][1000 genomes]
rs10821002	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10821003	0.94[ASN][1000 genomes]
rs10821004	0.96[ASN][1000 genomes]
rs10821005	0.94[ASN][1000 genomes]
rs10821007	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10821009	0.81[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10821010	0.80[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10821011	1.00[ASN][1000 genomes]
rs10821012	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10821014	0.99[ASN][1000 genomes]
rs10821015	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10821016	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10821017	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10992380	0.82[CHB][hapmap];0.87[MEX][hapmap]
rs10992382	0.85[CEU][hapmap];0.88[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs10992384	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs10992390	0.94[CHB][hapmap]
rs10992392	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[MEX][hapmap]
rs10992394	0.92[EUR][1000 genomes]
rs10992396	0.84[ASN][1000 genomes]
rs10992404	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992406	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992407	0.92[CEU][hapmap];0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs10992408	0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs10992409	0.81[ASN][1000 genomes]
rs10992412	0.85[ASN][1000 genomes]
rs10992413	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10992414	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10992416	0.94[ASN][1000 genomes]
rs10992417	0.94[ASN][1000 genomes]
rs10992418	0.82[ASN][1000 genomes]
rs10992419	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10992420	0.94[ASN][1000 genomes]
rs10992422	0.96[ASN][1000 genomes]
rs10992423	0.93[ASN][1000 genomes]
rs10992426	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992427	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10992430	0.80[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10992431	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10992432	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10992433	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992434	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10992436	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992437	1.00[ASN][1000 genomes]
rs10992438	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992441	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992442	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992443	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992444	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992445	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992447	0.92[CEU][hapmap]
rs10992448	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10992451	0.80[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992453	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10992456	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992460	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10992461	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10992462	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992469	0.83[JPT][hapmap]
rs10992475	0.87[EUR][1000 genomes]
rs1117670	0.85[CEU][hapmap];0.88[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs1125063	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1125064	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11533010	0.96[ASN][1000 genomes]
rs11535540	0.82[ASN][1000 genomes]
rs12236393	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12236516	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12236747	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12236754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12237216	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12238691	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs12683839	0.81[EUR][1000 genomes]
rs12683944	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12684076	0.89[ASN][1000 genomes]
rs12684587	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12685256	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12685257	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12685358	0.96[ASN][1000 genomes]
rs12685780	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12685791	0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12686058	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12686771	0.92[CEU][hapmap]
rs1323523	0.88[CHB][hapmap]
rs1326775	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs1407944	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1552908	0.84[MEX][hapmap]
rs1575460	0.88[CHB][hapmap]
rs16908555	0.85[CEU][hapmap]
rs16908560	0.84[CEU][hapmap]
rs1853427	0.87[EUR][1000 genomes]
rs1853428	0.85[CEU][hapmap]
rs1853468	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs1974004	0.85[CEU][hapmap]
rs1980705	0.84[MEX][hapmap]
rs2088055	0.83[AMR][1000 genomes]
rs2148537	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs2181584	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs2181586	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2277164	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2281888	0.84[MEX][hapmap]
rs2296080	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3203916	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3739605	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[ASN][1000 genomes]
rs4545157	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs556	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56111209	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56203846	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56311406	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56339669	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57421019	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57720404	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57737182	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58952648	0.94[ASN][1000 genomes]
rs60173654	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60457563	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60498616	0.98[ASN][1000 genomes]
rs6479426	0.85[CEU][hapmap];0.88[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs66493272	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs68022962	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68046436	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7031163	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7037961	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72618187	0.87[EUR][1000 genomes]
rs753802	0.81[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs753803	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs753804	1.00[ASN][1000 genomes]
rs7850075	0.85[CEU][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap]
rs7850871	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851947	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7856147	0.94[CHB][hapmap]
rs7857105	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[MEX][hapmap]
rs7857502	0.94[CHB][hapmap]
rs7860628	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7862106	0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7863741	0.83[AMR][1000 genomes]
rs7863882	0.85[CEU][hapmap];0.88[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs7863890	0.84[MEX][hapmap]
rs7869529	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7869603	0.98[ASN][1000 genomes]
rs7871537	0.86[JPT][hapmap]
rs7875050	0.81[CEU][hapmap];0.94[CHB][hapmap]
rs7875225	0.83[JPT][hapmap]
rs7875227	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8181065	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs878610	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs879812	0.84[MEX][hapmap]
rs912259	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs912261	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs971984	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs976320	0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs976321	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9775970	0.90[AMR][1000 genomes];0.94[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12236788	BICD2	Cis_1M	lymphoblastoid	RTeQTL
rs12236788	FBP1	cis	cerebellum	SCAN
rs12236788	CENPP	cis	multi-tissue	Pritchard
rs12236788	ANKRD19	cis	cerebellum	SCAN
rs12236788	C9orf89	cis	parietal	SCAN
rs12236788	CENPP	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95533400-95543200	Weak transcription	Esophagus	oesophagus
2	chr9:95537200-95543800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:95537600-95544000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:95538200-95543800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:95538800-95543600	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr9:95541200-95543200	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr9:95541400-95558600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:95542000-95543200	Enhancers	Primary monocytes fromperipheralblood	blood

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