Variant report

Variant	rs879812
Chromosome Location	chr9:95427070-95427071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95416446..95420766-chr9:95422078..95429343,12	MCF-7	breast:
2	chr9:95408645..95411080-chr9:95427015..95428755,2	MCF-7	breast:
3	chr9:95426803..95428983-chr9:95470405..95473212,2	K562	blood:
4	chr9:95427021..95427756-chr9:95526995..95527773,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185963	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1010823	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10820997	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10820998	0.82[JPT][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs10821000	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10821002	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10821007	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10821009	0.87[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10821010	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10821012	0.87[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10821015	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10821016	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992367	0.84[MEX][hapmap]
rs10992382	0.84[MEX][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs10992384	0.84[MEX][hapmap]
rs10992390	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10992392	0.82[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs10992394	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10992402	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10992403	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10992406	0.86[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes]
rs10992407	0.82[JPT][hapmap]
rs10992408	0.86[JPT][hapmap]
rs10992413	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10992419	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10992427	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992430	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992431	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992432	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992434	0.87[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992436	0.86[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992438	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992441	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992442	0.87[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992443	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992444	0.87[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992445	0.87[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10992448	0.84[MEX][hapmap]
rs10992451	0.87[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992456	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10992460	0.84[MEX][hapmap]
rs10992461	0.84[MEX][hapmap]
rs10992462	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10992469	0.96[MEX][hapmap]
rs10992472	0.80[EUR][1000 genomes]
rs1117670	0.83[ASW][hapmap];0.84[MEX][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs1125063	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1125064	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12236013	0.81[ASN][1000 genomes]
rs12236393	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12236516	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12236747	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12237216	0.81[AMR][1000 genomes]
rs12683839	0.88[EUR][1000 genomes]
rs12683944	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12685080	0.93[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12685256	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12685257	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12685780	0.87[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12685791	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12686058	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1326775	0.84[MEX][hapmap]
rs1552908	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]
rs17366488	0.82[ASN][1000 genomes]
rs1810696	0.92[MEX][hapmap]
rs1853468	0.84[MEX][hapmap]
rs1874128	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1980705	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2038686	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2088055	0.81[AMR][1000 genomes]
rs2131919	0.84[MEX][hapmap]
rs2148537	0.84[MEX][hapmap]
rs2181586	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2274413	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2277164	0.83[EUR][1000 genomes]
rs2277166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2281888	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2296080	0.87[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3203916	0.87[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3739605	0.84[MEX][hapmap]
rs41266683	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4545157	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs556	0.87[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56111209	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56203846	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56339669	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57421019	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57720404	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58045868	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60173654	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60457563	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6479426	0.83[ASW][hapmap];0.84[MEX][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs66493272	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67601697	0.80[ASN][1000 genomes]
rs68022962	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs68046436	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7031163	0.80[MEX][hapmap]
rs7037961	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs753802	0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs753803	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs754600	0.84[ASN][1000 genomes]
rs7853617	0.81[ASN][1000 genomes]
rs7856147	0.82[JPT][hapmap]
rs7857105	0.82[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs7857502	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7862106	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7863882	0.84[MEX][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs7863890	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7864889	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7869529	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7875050	0.82[JPT][hapmap]
rs7875227	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8181065	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs878610	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs912259	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs912261	0.83[ASW][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs912264	0.81[CHB][hapmap]
rs971984	0.84[MEX][hapmap]
rs976320	0.81[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs976321	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs879812	BICD2	Cis_1M	lymphoblastoid	RTeQTL
rs879812	ANKRD19	cis	parietal	SCAN
rs879812	CENPP	cis	parietal	SCAN
rs879812	C9orf89	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95380800-95429000	Weak transcription	Stomach Mucosa	stomach
2	chr9:95409800-95431000	Weak transcription	Fetal Kidney	kidney
3	chr9:95411000-95431400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:95411800-95427400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr9:95412000-95428400	Weak transcription	K562	blood
6	chr9:95412000-95431000	Weak transcription	Fetal Brain Male	brain
7	chr9:95412400-95431200	Weak transcription	Small Intestine	intestine
8	chr9:95417800-95431000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:95418000-95428800	Weak transcription	Fetal Lung	lung
10	chr9:95418000-95431000	Weak transcription	Psoas Muscle	Psoas
11	chr9:95418200-95428600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:95418600-95431000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:95420800-95428200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:95420800-95428200	Weak transcription	Fetal Intestine Large	intestine
15	chr9:95420800-95428200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:95420800-95428400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:95420800-95428400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr9:95420800-95429000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:95420800-95430800	Weak transcription	HSMMtube	muscle
20	chr9:95420800-95431000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:95420800-95431000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:95421000-95428200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr9:95421000-95428200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr9:95421000-95428400	Weak transcription	Ovary	ovary
25	chr9:95421200-95428200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr9:95421200-95428400	Weak transcription	Aorta	Aorta
27	chr9:95421200-95430800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr9:95421200-95430800	Weak transcription	Colon Smooth Muscle	Colon
29	chr9:95421200-95431000	Weak transcription	Colonic Mucosa	Colon
30	chr9:95421400-95428200	Weak transcription	Dnd41	blood
31	chr9:95421400-95428400	Weak transcription	A549	lung
32	chr9:95422200-95429800	Strong transcription	Fetal Intestine Small	intestine
33	chr9:95422400-95431200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr9:95422600-95427200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr9:95422800-95428800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:95422800-95430800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:95422800-95431000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr9:95422800-95431400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:95423000-95428800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:95423400-95429800	Strong transcription	Fetal Stomach	stomach
41	chr9:95424000-95428200	Weak transcription	Osteobl	bone
42	chr9:95424000-95429800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr9:95424200-95427200	Strong transcription	NHEK	skin
44	chr9:95424200-95427600	Weak transcription	HSMM	muscle
45	chr9:95424200-95430600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr9:95424400-95428400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:95425200-95427400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:95425200-95430000	Strong transcription	Fetal Muscle Leg	muscle
49	chr9:95425400-95428600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:95425600-95427200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links