Variant report

Variant	rs12236747
Chromosome Location	chr9:95512185-95512186
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95506780..95509638-chr9:95511921..95514054,2	K562	blood:
2	chr9:95431607..95434471-chr9:95510913..95512598,2	K562	blood:
3	chr9:95510041..95513567-chr9:95525566..95528932,4	K562	blood:
4	chr9:95504668..95516688-chr9:95523327..95528935,18	MCF-7	breast:
5	chr9:94894055..94896272-chr9:95510908..95513385,2	K562	blood:
6	chr9:95431607..95434580-chr9:95510913..95513196,3	K562	blood:

Variant related genes	Relation type
ENSG00000127080	Chromatin interaction
ENSG00000185963	Chromatin interaction
ENSG00000234537	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1010823	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821000	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10821001	0.83[ASN][1000 genomes]
rs10821002	0.98[AMR][1000 genomes];0.97[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	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821009	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821010	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821011	0.85[ASN][1000 genomes]
rs10821012	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821016	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992402	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10992403	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10992404	0.80[EUR][1000 genomes]
rs10992406	0.80[EUR][1000 genomes]
rs10992413	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[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	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10992419	0.98[AMR][1000 genomes];0.97[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];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10992427	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992430	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992431	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992432	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992433	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10992434	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992436	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992437	0.85[ASN][1000 genomes]
rs10992438	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992441	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992442	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992443	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992444	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992445	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[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];1.00[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];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992472	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1125063	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125064	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11533010	0.83[ASN][1000 genomes]
rs11535540	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12236393	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12236516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236754	0.85[ASN][1000 genomes]
rs12236788	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12237216	0.80[EUR][1000 genomes]
rs12238691	0.84[ASN][1000 genomes]
rs12683839	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12683944	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12685257	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685791	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12686058	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1407944	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1552908	0.90[AMR][1000 genomes]
rs1874128	0.86[AMR][1000 genomes]
rs1980705	0.85[AMR][1000 genomes]
rs2038686	0.86[AMR][1000 genomes]
rs2181584	0.83[ASN][1000 genomes]
rs2181586	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274413	0.86[AMR][1000 genomes]
rs2277164	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277166	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2281888	0.85[AMR][1000 genomes]
rs2296080	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3203916	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3739605	0.82[ASN][1000 genomes]
rs41266683	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4545157	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56111209	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56203846	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56311406	0.85[ASN][1000 genomes]
rs56339669	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57421019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57720404	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57737182	0.85[ASN][1000 genomes]
rs58045868	0.83[AMR][1000 genomes]
rs58952648	0.82[ASN][1000 genomes]
rs60173654	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60457563	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60498616	0.84[ASN][1000 genomes]
rs66493272	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68022962	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68046436	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031163	0.85[ASN][1000 genomes]
rs7037961	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs753802	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753803	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753804	0.85[ASN][1000 genomes]
rs7850871	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7851947	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7860628	0.83[ASN][1000 genomes]
rs7862106	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7863890	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7864889	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7869529	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7869603	0.84[ASN][1000 genomes]
rs7875227	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8181065	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs878610	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879812	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs912259	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912261	0.80[EUR][1000 genomes]
rs976320	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976321	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9775970	0.83[AFR][1000 genomes];0.82[AMR][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
rs12236747	BICD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95502400-95516400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr9:95503400-95518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:95503600-95514400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr9:95503600-95514400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr9:95503600-95517800	Weak transcription	Fetal Intestine Large	intestine
6	chr9:95503800-95523800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr9:95507200-95512400	Enhancers	Lung	lung
8	chr9:95507200-95512600	Enhancers	Left Ventricle	heart
9	chr9:95507200-95512600	Enhancers	Ovary	ovary
10	chr9:95507400-95512200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr9:95507400-95512400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:95507400-95512400	Enhancers	Right Atrium	heart
13	chr9:95507400-95512600	Enhancers	Placenta	Placenta
14	chr9:95507400-95512600	Enhancers	Right Ventricle	heart
15	chr9:95507400-95512800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:95507400-95512800	Enhancers	Fetal Heart	heart
17	chr9:95507400-95513200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr9:95507400-95513800	Enhancers	Primary B cells from peripheral blood	blood
19	chr9:95507600-95512400	Enhancers	Fetal Muscle Trunk	muscle
20	chr9:95507600-95512600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr9:95508000-95512200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:95508000-95517800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr9:95508200-95512400	Enhancers	NHLF	lung
24	chr9:95508200-95515000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:95508200-95517800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:95508200-95517800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:95508400-95512200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:95508400-95512200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr9:95508400-95514400	Weak transcription	Primary T cells from cord blood	blood
30	chr9:95508400-95516400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr9:95508600-95512400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:95508600-95512800	Enhancers	HSMM	muscle
33	chr9:95508600-95513000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr9:95508800-95512200	Enhancers	HMEC	breast
35	chr9:95508800-95512400	Enhancers	Psoas Muscle	Psoas
36	chr9:95508800-95512400	Enhancers	NHDF-Ad	bronchial
37	chr9:95508800-95512600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr9:95508800-95512800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:95508800-95512800	Enhancers	Adipose Nuclei	Adipose
40	chr9:95508800-95512800	Enhancers	Osteobl	bone
41	chr9:95509000-95512200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:95509000-95512200	Genic enhancers	Fetal Stomach	stomach
43	chr9:95509000-95512400	Enhancers	Stomach Mucosa	stomach
44	chr9:95509000-95512600	Enhancers	Colonic Mucosa	Colon
45	chr9:95509000-95513000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:95509000-95513000	Enhancers	HSMMtube	muscle
47	chr9:95509200-95512200	Enhancers	Brain Angular Gyrus	brain
48	chr9:95509200-95512400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr9:95509200-95512400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr9:95509400-95512400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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