Variant report

Variant	rs56111209
Chromosome Location	chr9:95534755-95534756
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95430418..95433752-chr9:95532956..95535210,3	MCF-7	breast:
2	chr9:95533275..95536174-chr9:95541211..95543902,2	MCF-7	breast:
3	chr9:95524574..95529988-chr9:95531032..95538459,18	K562	blood:
4	chr9:95430857..95432661-chr9:95532674..95534827,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185963	Chromatin interaction
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1010823	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821000	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10821001	0.83[ASN][1000 genomes]
rs10821002	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821003	0.83[ASN][1000 genomes]
rs10821004	0.83[ASN][1000 genomes]
rs10821005	0.82[ASN][1000 genomes]
rs10821007	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821009	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821010	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821011	0.85[ASN][1000 genomes]
rs10821012	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821014	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10821015	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821016	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992402	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10992403	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10992413	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992414	0.81[ASN][1000 genomes]
rs10992416	0.83[ASN][1000 genomes]
rs10992417	0.83[ASN][1000 genomes]
rs10992418	0.96[ASN][1000 genomes]
rs10992419	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992420	0.83[ASN][1000 genomes]
rs10992422	0.83[ASN][1000 genomes]
rs10992423	0.83[ASN][1000 genomes]
rs10992426	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10992427	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992430	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992431	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992432	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992433	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10992434	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992436	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992437	0.85[ASN][1000 genomes]
rs10992438	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992441	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992442	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992443	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992444	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992445	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992448	0.84[ASN][1000 genomes]
rs10992451	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992453	0.85[ASN][1000 genomes]
rs10992454	0.90[AFR][1000 genomes]
rs10992456	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992460	0.85[ASN][1000 genomes]
rs10992461	0.85[ASN][1000 genomes]
rs10992462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992469	0.84[AMR][1000 genomes]
rs10992472	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1125063	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125064	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11533010	0.83[ASN][1000 genomes]
rs11535540	0.96[ASN][1000 genomes]
rs12236393	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12236516	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236747	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236754	0.85[ASN][1000 genomes]
rs12236788	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12238691	0.84[ASN][1000 genomes]
rs12683839	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12683944	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12684587	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12685080	0.89[ASN][1000 genomes]
rs12685256	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12685257	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685358	0.83[ASN][1000 genomes]
rs12685780	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685791	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12686058	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1407944	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1552908	0.86[AMR][1000 genomes]
rs1555574	0.84[AMR][1000 genomes]
rs1874128	0.82[AMR][1000 genomes]
rs1980705	0.81[AMR][1000 genomes]
rs2038686	0.82[AMR][1000 genomes]
rs2181584	0.83[ASN][1000 genomes]
rs2181586	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274413	0.82[AMR][1000 genomes]
rs2277164	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277166	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2281888	0.81[AMR][1000 genomes]
rs2296080	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3203916	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3739605	0.82[ASN][1000 genomes]
rs41266683	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4545157	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56203846	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56311406	0.85[ASN][1000 genomes]
rs56339669	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57421019	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57720404	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57737182	0.85[ASN][1000 genomes]
rs58952648	0.82[ASN][1000 genomes]
rs60173654	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60457563	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60498616	0.84[ASN][1000 genomes]
rs66493272	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68022962	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68046436	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031163	0.85[ASN][1000 genomes]
rs7037961	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs753802	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753803	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753804	0.85[ASN][1000 genomes]
rs7850871	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7851947	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7860628	0.83[ASN][1000 genomes]
rs7862106	0.96[ASN][1000 genomes]
rs7863890	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7864889	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7869529	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7869603	0.84[ASN][1000 genomes]
rs7871537	0.84[AMR][1000 genomes]
rs7875227	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8181065	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs878610	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879812	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs912259	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976320	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976321	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9775970	0.83[AFR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56111209	BICD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95528800-95536400	Weak transcription	HSMM	muscle
2	chr9:95530800-95534800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:95532800-95534800	Enhancers	NHEK	skin
4	chr9:95533000-95535000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:95533000-95536600	Weak transcription	Brain Hippocampus Middle	brain
6	chr9:95533200-95535000	Enhancers	Fetal Heart	heart
7	chr9:95533200-95536000	Weak transcription	Right Atrium	heart
8	chr9:95533200-95536200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:95533200-95536400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:95533200-95536400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:95533200-95536400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr9:95533200-95536600	Weak transcription	Brain Anterior Caudate	brain
13	chr9:95533200-95537600	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr9:95533200-95541200	Weak transcription	Left Ventricle	heart
15	chr9:95533400-95536600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr9:95533400-95541200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:95533400-95543200	Weak transcription	Esophagus	oesophagus
18	chr9:95533600-95534800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:95533600-95536400	Weak transcription	Primary B cells from cord blood	blood
20	chr9:95533600-95537800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr9:95533800-95536600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr9:95533800-95537400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:95533800-95537800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:95534000-95537600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr9:95534000-95537800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr9:95534400-95536200	Weak transcription	HMEC	breast
27	chr9:95534400-95536400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr9:95534600-95535000	Flanking Active TSS	HepG2	liver

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