Variant report

Variant	rs12683944
Chromosome Location	chr9:95508431-95508432
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:95506780..95509638-chr9:95511921..95514054,2	K562	blood:
2	chr9:95489380..95491357-chr9:95508006..95509721,2	K562	blood:
3	chr9:95500735..95502808-chr9:95507809..95510378,3	MCF-7	breast:
4	chr9:95501433..95503464-chr9:95508395..95511050,2	K562	blood:
5	chr9:95478702..95480527-chr9:95507539..95509486,2	K562	blood:
6	chr9:95429103..95431144-chr9:95506974..95509653,2	MCF-7	breast:
7	chr9:95504029..95507342-chr9:95507599..95511465,3	MCF-7	breast:
8	chr9:95505768..95509584-chr9:95524404..95527885,5	K562	blood:
9	chr9:95504668..95516688-chr9:95523327..95528935,18	MCF-7	breast:
10	chr9:95499325..95502717-chr9:95506980..95509904,5	MCF-7	breast:
11	chr9:95507487..95509830-chr9:95526324..95529245,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185963	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1010823	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821000	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10821001	0.82[ASN][1000 genomes]
rs10821002	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821003	0.82[ASN][1000 genomes]
rs10821004	0.82[ASN][1000 genomes]
rs10821005	0.81[ASN][1000 genomes]
rs10821007	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821009	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821010	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821011	0.85[ASN][1000 genomes]
rs10821012	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821014	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10821015	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821016	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992402	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10992403	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10992404	0.80[EUR][1000 genomes]
rs10992406	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992413	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10992414	0.81[ASN][1000 genomes]
rs10992416	0.82[ASN][1000 genomes]
rs10992417	0.82[ASN][1000 genomes]
rs10992418	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10992419	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992420	0.82[ASN][1000 genomes]
rs10992422	0.82[ASN][1000 genomes]
rs10992423	0.82[ASN][1000 genomes]
rs10992426	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10992427	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992430	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992431	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992432	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992433	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10992434	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992436	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992437	0.85[ASN][1000 genomes]
rs10992438	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992441	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992442	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992448	0.83[ASN][1000 genomes]
rs10992451	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992453	0.85[ASN][1000 genomes]
rs10992454	0.87[AFR][1000 genomes]
rs10992456	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992460	0.85[ASN][1000 genomes]
rs10992461	0.85[ASN][1000 genomes]
rs10992462	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992472	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1125063	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1125064	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11533010	0.82[ASN][1000 genomes]
rs11535540	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12236393	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12236516	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12236747	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12236754	0.85[ASN][1000 genomes]
rs12236788	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12237216	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12238691	0.83[ASN][1000 genomes]
rs12683839	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12684587	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12685080	0.89[ASN][1000 genomes]
rs12685256	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12685257	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12685358	0.82[ASN][1000 genomes]
rs12685780	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12685791	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12686058	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1407944	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1552908	0.92[AMR][1000 genomes]
rs1874128	0.88[AMR][1000 genomes]
rs1980705	0.87[AMR][1000 genomes]
rs2038686	0.88[AMR][1000 genomes]
rs2088055	0.82[AMR][1000 genomes]
rs2181584	0.82[ASN][1000 genomes]
rs2181586	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274413	0.88[AMR][1000 genomes]
rs2277164	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277166	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2281888	0.87[AMR][1000 genomes]
rs2296080	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3203916	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3739605	0.81[ASN][1000 genomes]
rs41266683	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4545157	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs556	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56111209	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56203846	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56311406	0.85[ASN][1000 genomes]
rs56339669	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57421019	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57720404	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57737182	0.85[ASN][1000 genomes]
rs58045868	0.85[AMR][1000 genomes]
rs58952648	0.81[ASN][1000 genomes]
rs60173654	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60457563	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60498616	0.83[ASN][1000 genomes]
rs66493272	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68022962	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68046436	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7031163	0.85[ASN][1000 genomes]
rs7037961	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs753802	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs753803	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs753804	0.85[ASN][1000 genomes]
rs7850871	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7851947	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7860628	0.82[ASN][1000 genomes]
rs7862106	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7863890	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7864889	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7869529	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7869603	0.83[ASN][1000 genomes]
rs7875227	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8181065	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs878610	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs879812	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs912259	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs912261	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs976320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs976321	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9775970	0.84[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
rs12683944	BICD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95485600-95511600	Weak transcription	Aorta	Aorta
2	chr9:95498600-95510200	Weak transcription	Hela-S3	cervix
3	chr9:95502000-95511200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:95502200-95511200	Weak transcription	Fetal Brain Male	brain
5	chr9:95502200-95511600	Weak transcription	Fetal Brain Female	brain
6	chr9:95502400-95516400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:95503400-95508800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:95503400-95508800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr9:95503400-95508800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr9:95503400-95508800	Weak transcription	Fetal Kidney	kidney
11	chr9:95503400-95509000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:95503400-95511600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:95503400-95518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:95503600-95508800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:95503600-95508800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:95503600-95508800	Weak transcription	Adipose Nuclei	Adipose
17	chr9:95503600-95508800	Weak transcription	Liver	Liver
18	chr9:95503600-95508800	Weak transcription	NHDF-Ad	bronchial
19	chr9:95503600-95508800	Weak transcription	Osteobl	bone
20	chr9:95503600-95509000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:95503600-95509000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:95503600-95509800	Weak transcription	Fetal Intestine Small	intestine
23	chr9:95503600-95510400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr9:95503600-95514400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr9:95503600-95514400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr9:95503600-95517800	Weak transcription	Fetal Intestine Large	intestine
27	chr9:95503800-95508800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:95503800-95508800	Weak transcription	HMEC	breast
29	chr9:95503800-95523800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr9:95504200-95509000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:95504400-95509800	Weak transcription	NHEK	skin
32	chr9:95505400-95509800	Weak transcription	GM12878-XiMat	blood
33	chr9:95505400-95510000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr9:95506000-95510400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr9:95506600-95508800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:95507200-95508800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:95507200-95512400	Enhancers	Lung	lung
38	chr9:95507200-95512600	Enhancers	Left Ventricle	heart
39	chr9:95507200-95512600	Enhancers	Ovary	ovary
40	chr9:95507400-95508600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr9:95507400-95508600	Enhancers	Brain Substantia Nigra	brain
42	chr9:95507400-95508800	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr9:95507400-95510000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr9:95507400-95510000	Enhancers	Fetal Muscle Leg	muscle
45	chr9:95507400-95510200	Enhancers	Spleen	Spleen
46	chr9:95507400-95510400	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr9:95507400-95510800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr9:95507400-95510800	Enhancers	HUVEC	blood vessel
49	chr9:95507400-95511000	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr9:95507400-95511200	Enhancers	K562	blood

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