Variant report

Variant	rs2277164
Chromosome Location	chr9:95526667-95526668
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95086140..95089391-chr9:95526124..95530104,3	K562	blood:
2	chr9:95428069..95433526-chr9:95524054..95531235,7	MCF-7	breast:
3	chr9:95432219..95434684-chr9:95525652..95527897,3	K562	blood:
4	chr6:30180933..30181555-chr9:95526315..95527180,2	Hela-S3	cervix:
5	chr9:95054612..95057091-chr9:95526187..95528018,2	K562	blood:
6	chr9:95430814..95434525-chr9:95525652..95528883,5	K562	blood:
7	chr7:43908068..43910411-chr9:95526104..95528854,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239183	Chromatin interaction
ENSG00000062582	Chromatin interaction
ENSG00000127080	Chromatin interaction
ENSG00000188312	Chromatin interaction
ENSG00000196305	Chromatin interaction
ENSG00000198000	Chromatin interaction
ENSG00000234127	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1010823	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821000	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10821001	0.87[ASN][1000 genomes]
rs10821002	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10821003	0.87[ASN][1000 genomes]
rs10821004	0.87[ASN][1000 genomes]
rs10821005	0.85[ASN][1000 genomes]
rs10821007	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821009	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10821010	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821011	0.89[ASN][1000 genomes]
rs10821012	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821014	0.89[ASN][1000 genomes]
rs10821015	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821016	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821017	0.82[EUR][1000 genomes]
rs10992394	0.82[EUR][1000 genomes]
rs10992402	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10992403	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10992404	0.85[EUR][1000 genomes]
rs10992406	0.85[EUR][1000 genomes]
rs10992413	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10992414	0.85[ASN][1000 genomes]
rs10992416	0.87[ASN][1000 genomes]
rs10992417	0.87[ASN][1000 genomes]
rs10992418	0.92[ASN][1000 genomes]
rs10992419	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992420	0.87[ASN][1000 genomes]
rs10992422	0.87[ASN][1000 genomes]
rs10992423	0.87[ASN][1000 genomes]
rs10992426	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10992427	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992430	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992431	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992432	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992433	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10992434	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992436	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992437	0.89[ASN][1000 genomes]
rs10992438	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992441	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10992442	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992443	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992444	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992445	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992448	0.88[ASN][1000 genomes]
rs10992451	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992453	0.89[ASN][1000 genomes]
rs10992456	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992460	0.89[ASN][1000 genomes]
rs10992461	0.89[ASN][1000 genomes]
rs10992462	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992472	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1125063	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1125064	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11533010	0.87[ASN][1000 genomes]
rs11535540	0.92[ASN][1000 genomes]
rs12236393	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12236516	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12236747	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12236754	0.89[ASN][1000 genomes]
rs12236788	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12237216	0.85[EUR][1000 genomes]
rs12238691	0.88[ASN][1000 genomes]
rs12683839	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12683944	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12684587	0.89[ASN][1000 genomes]
rs12685080	0.85[ASN][1000 genomes]
rs12685256	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12685257	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12685358	0.87[ASN][1000 genomes]
rs12685780	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12685791	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12686058	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1407944	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1552908	0.84[AMR][1000 genomes]
rs2181584	0.87[ASN][1000 genomes]
rs2181586	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2277166	0.83[EUR][1000 genomes]
rs2296080	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3203916	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3739605	0.86[ASN][1000 genomes]
rs41266683	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4545157	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs556	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56111209	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56203846	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56311406	0.89[ASN][1000 genomes]
rs56339669	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57421019	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57720404	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57737182	0.89[ASN][1000 genomes]
rs58952648	0.85[ASN][1000 genomes]
rs60173654	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60457563	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60498616	0.88[ASN][1000 genomes]
rs66493272	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68022962	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68046436	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7031163	0.89[ASN][1000 genomes]
rs7037961	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs753802	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs753803	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs753804	0.89[ASN][1000 genomes]
rs7850871	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7851947	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7860628	0.86[ASN][1000 genomes]
rs7862106	0.92[ASN][1000 genomes]
rs7863890	0.83[EUR][1000 genomes]
rs7864889	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7869529	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7869603	0.88[ASN][1000 genomes]
rs7875227	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8181065	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs878610	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs879812	0.83[EUR][1000 genomes]
rs912259	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs912261	0.85[EUR][1000 genomes]
rs976320	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs976321	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9775970	0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2277164	BICD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95525000-95528000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:95525200-95528200	Active TSS	HSMM	muscle
3	chr9:95525400-95528400	Active TSS	A549	lung
4	chr9:95525600-95527600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:95525600-95528000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr9:95525600-95528600	Active TSS	Fetal Kidney	kidney
7	chr9:95525600-95528600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr9:95525800-95527800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr9:95525800-95527800	Active TSS	Rectal Smooth Muscle	rectum
10	chr9:95525800-95527800	Active TSS	Small Intestine	intestine
11	chr9:95525800-95528000	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr9:95525800-95528000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:95525800-95528000	Active TSS	HSMMtube	muscle
14	chr9:95525800-95528000	Active TSS	NHDF-Ad	bronchial
15	chr9:95525800-95528200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:95525800-95528200	Active TSS	Aorta	Aorta
17	chr9:95525800-95528200	Active TSS	Fetal Intestine Large	intestine
18	chr9:95525800-95528400	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr9:95525800-95528400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:95526000-95526800	Active TSS	Brain Germinal Matrix	brain
21	chr9:95526000-95527800	Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr9:95526000-95527800	Active TSS	GM12878-XiMat	blood
23	chr9:95526000-95527800	Active TSS	Monocytes-CD14+_RO01746	blood
24	chr9:95526000-95527800	Active TSS	NHEK	skin
25	chr9:95526000-95527800	Active TSS	NHLF	lung
26	chr9:95526000-95528000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:95526000-95528000	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr9:95526000-95528000	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr9:95526000-95528000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:95526000-95528000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:95526000-95528000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:95526000-95528000	Active TSS	Muscle Satellite Cultured Cells	--
33	chr9:95526000-95528000	Active TSS	Colon Smooth Muscle	Colon
34	chr9:95526000-95528000	Active TSS	Fetal Intestine Small	intestine
35	chr9:95526000-95528000	Active TSS	Lung	lung
36	chr9:95526000-95528000	Active TSS	HepG2	liver
37	chr9:95526000-95528000	Active TSS	NH-A	brain
38	chr9:95526000-95528000	Active TSS	Osteobl	bone
39	chr9:95526000-95528200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr9:95526000-95528200	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr9:95526000-95528200	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr9:95526000-95528200	Active TSS	Ovary	ovary
43	chr9:95526000-95528400	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr9:95526000-95528400	Active TSS	Left Ventricle	heart
45	chr9:95526000-95528400	Active TSS	Psoas Muscle	Psoas
46	chr9:95526000-95528600	Active TSS	Fetal Lung	lung
47	chr9:95526200-95526800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr9:95526200-95527000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:95526200-95527000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr9:95526200-95527000	Active TSS	Fetal Brain Male	brain

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