Variant report

Variant	rs1552908
Chromosome Location	chr9:95373884-95373885
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95373177..95375110-chr9:95377702..95380287,2	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1010823	0.88[AMR][1000 genomes]
rs10491806	0.80[JPT][hapmap]
rs10820997	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs10820998	0.84[MEX][hapmap]
rs10821000	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10821002	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10821007	0.92[AMR][1000 genomes]
rs10821009	0.87[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes]
rs10821010	0.87[CEU][hapmap];0.92[AMR][1000 genomes]
rs10821012	0.87[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes]
rs10821015	0.90[AMR][1000 genomes]
rs10821016	0.88[AMR][1000 genomes]
rs10992367	0.80[JPT][hapmap];0.84[MEX][hapmap]
rs10992382	0.80[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10992384	0.85[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs10992392	0.84[MEX][hapmap]
rs10992402	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10992403	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10992413	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992419	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992427	0.92[AMR][1000 genomes]
rs10992430	0.87[CEU][hapmap];0.92[AMR][1000 genomes]
rs10992431	0.87[CEU][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes]
rs10992432	0.87[CEU][hapmap];0.92[AMR][1000 genomes]
rs10992434	0.82[ASW][hapmap];0.87[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes]
rs10992436	0.92[AMR][1000 genomes]
rs10992438	0.92[AMR][1000 genomes]
rs10992441	0.92[AMR][1000 genomes]
rs10992442	0.82[ASW][hapmap];0.87[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes]
rs10992443	0.87[CEU][hapmap];0.92[AMR][1000 genomes]
rs10992444	0.87[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes]
rs10992445	0.87[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes]
rs10992448	0.84[MEX][hapmap]
rs10992451	0.87[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes]
rs10992456	0.88[AMR][1000 genomes]
rs10992460	0.84[MEX][hapmap]
rs10992461	0.84[MEX][hapmap]
rs10992462	0.86[AMR][1000 genomes]
rs10992469	0.96[MEX][hapmap]
rs1117670	0.85[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1125063	0.87[CEU][hapmap];0.88[AMR][1000 genomes]
rs1125064	0.87[CEU][hapmap];0.88[AMR][1000 genomes]
rs12236393	0.87[CEU][hapmap];0.92[AMR][1000 genomes]
rs12236516	0.87[CEU][hapmap];0.90[AMR][1000 genomes]
rs12236747	0.90[AMR][1000 genomes]
rs12683839	0.82[AMR][1000 genomes]
rs12683944	0.92[AMR][1000 genomes]
rs12685080	0.86[CHB][hapmap]
rs12685256	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12685257	0.87[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes]
rs12685780	0.87[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes]
rs12685791	0.85[CEU][hapmap];0.88[AMR][1000 genomes]
rs12686058	0.90[AMR][1000 genomes]
rs12686780	0.85[ASN][1000 genomes]
rs12686781	0.85[ASN][1000 genomes]
rs1326775	0.80[JPT][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs1575460	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1810696	0.92[MEX][hapmap]
rs1853468	0.85[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs1874128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1980705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038686	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2088055	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2131919	0.80[JPT][hapmap];0.84[MEX][hapmap]
rs2148537	0.85[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs2181586	0.87[CEU][hapmap];0.92[AMR][1000 genomes]
rs2274413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277164	0.84[AMR][1000 genomes]
rs2277166	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2281888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296080	0.87[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes]
rs3203916	0.87[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes]
rs3739605	0.84[MEX][hapmap]
rs41266683	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4545157	0.85[AMR][1000 genomes]
rs556	0.87[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes]
rs56111209	0.86[AMR][1000 genomes]
rs56203846	0.92[AMR][1000 genomes]
rs56339669	0.92[AMR][1000 genomes]
rs57421019	0.90[AMR][1000 genomes]
rs57720404	0.90[AMR][1000 genomes]
rs58045868	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60173654	0.92[AMR][1000 genomes]
rs60457563	0.86[AMR][1000 genomes]
rs6479426	0.85[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66493272	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs68022962	0.86[AMR][1000 genomes]
rs68046436	0.92[AMR][1000 genomes]
rs7031163	0.80[MEX][hapmap]
rs7037961	0.92[AMR][1000 genomes]
rs753802	0.92[AMR][1000 genomes]
rs753803	0.87[CEU][hapmap];0.92[AMR][1000 genomes]
rs7857105	0.84[MEX][hapmap]
rs7863882	0.80[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7863890	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7864889	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7869529	0.92[AMR][1000 genomes]
rs7875227	0.92[AMR][1000 genomes]
rs8181065	0.87[CEU][hapmap];0.92[AMR][1000 genomes]
rs878610	0.88[AMR][1000 genomes]
rs879812	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs912259	0.91[AMR][1000 genomes]
rs912261	0.84[MEX][hapmap]
rs912264	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs971984	0.85[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs976320	0.81[YRI][hapmap];0.92[AMR][1000 genomes]
rs976321	0.90[AMR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1552908	BICD2	Cis_1M	lymphoblastoid	RTeQTL
rs1552908	C9orf89	cis	cerebellum	SCAN
rs1552908	CENPP	cis	parietal	SCAN
rs1552908	ANKRD19	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95363400-95374000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:95363400-95396000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:95366400-95375000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:95367400-95380600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:95369800-95374200	Weak transcription	Liver	Liver
6	chr9:95369800-95374200	Weak transcription	GM12878-XiMat	blood
7	chr9:95370200-95376200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:95370600-95394000	Weak transcription	Psoas Muscle	Psoas
9	chr9:95370800-95374200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr9:95370800-95377800	Weak transcription	Fetal Brain Male	brain
11	chr9:95370800-95380400	Weak transcription	Fetal Heart	heart
12	chr9:95371200-95375200	Weak transcription	NH-A	brain
13	chr9:95371200-95379800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr9:95371400-95398200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr9:95371600-95374000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr9:95371800-95374000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr9:95371800-95374000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:95371800-95374000	Weak transcription	Pancreas	Pancrea
19	chr9:95371800-95374200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr9:95371800-95376000	Weak transcription	Brain Angular Gyrus	brain
21	chr9:95371800-95377000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:95371800-95377400	Weak transcription	Fetal Kidney	kidney
23	chr9:95371800-95377600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr9:95371800-95379800	Weak transcription	Stomach Mucosa	stomach
25	chr9:95371800-95382400	Weak transcription	Right Atrium	heart
26	chr9:95371800-95399000	Weak transcription	Aorta	Aorta
27	chr9:95371800-95407400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr9:95372000-95374000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr9:95372000-95374000	Weak transcription	Colonic Mucosa	Colon
30	chr9:95372000-95374200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr9:95372000-95380200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:95372000-95394200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:95372200-95374000	Weak transcription	Primary B cells from cord blood	blood
34	chr9:95372200-95375400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr9:95372200-95380400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr9:95372400-95374400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr9:95372400-95383400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:95372600-95374200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr9:95372600-95374400	Enhancers	HSMMtube	muscle
40	chr9:95372600-95381400	Genic enhancers	Fetal Stomach	stomach
41	chr9:95372600-95383200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:95372800-95374000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:95372800-95374000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:95372800-95374200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr9:95372800-95374400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr9:95372800-95374400	Genic enhancers	Placenta	Placenta
47	chr9:95372800-95374400	Weak transcription	HUVEC	blood vessel
48	chr9:95372800-95374600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:95372800-95374600	Genic enhancers	Adipose Nuclei	Adipose
50	chr9:95372800-95374600	Strong transcription	Brain Cingulate Gyrus	brain

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