Variant report

Variant	rs953230
Chromosome Location	chr11:46064974-46064975
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:46063923..46066658-chr11:46067214..46069257,2	MCF-7	breast:
2	chr11:46060552..46062778-chr11:46063015..46065968,2	MCF-7	breast:
3	chr11:46063771..46065667-chr11:46071208..46072854,2	K562	blood:
4	chr11:46064941..46067349-chr19:13956189..13958474,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1976182	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2860404	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945999	0.83[MEX][hapmap]
rs2946003	0.81[JPT][hapmap]
rs2959084	0.95[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959087	0.83[YRI][hapmap]
rs2959090	0.84[YRI][hapmap]
rs2959091	0.84[YRI][hapmap]
rs4073513	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144718	0.81[CHD][hapmap];0.83[MEX][hapmap];0.84[YRI][hapmap]
rs4237660	0.81[CHD][hapmap];0.84[YRI][hapmap]
rs4756051	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs4756055	1.00[ASW][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7108186	0.81[CHD][hapmap];0.87[MEX][hapmap]
rs7112677	0.83[ASN][1000 genomes]
rs7114506	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128184	0.81[CHD][hapmap]
rs7926314	0.81[CHD][hapmap]
rs7948502	0.81[CHD][hapmap]
rs7950391	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs923530	0.97[ASN][1000 genomes]
rs939107	0.81[CHD][hapmap]
rs950105	0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs953230	ARHGAP1	cis	parietal	SCAN
rs953230	C11orf96	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46001400-46070400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:46022000-46074600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr11:46039200-46077200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:46039400-46096800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr11:46041000-46066200	Weak transcription	Liver	Liver
6	chr11:46041000-46071000	Weak transcription	Placenta	Placenta
7	chr11:46041200-46070800	Weak transcription	Thymus	Thymus
8	chr11:46041400-46086600	Weak transcription	Fetal Intestine Large	intestine
9	chr11:46042000-46065000	Weak transcription	Pancreas	Pancrea
10	chr11:46042000-46071000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:46042000-46071000	Weak transcription	Brain Angular Gyrus	brain
12	chr11:46043200-46071000	Weak transcription	Lung	lung
13	chr11:46043200-46086800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr11:46044400-46071000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr11:46044400-46071200	Weak transcription	Fetal Intestine Small	intestine
16	chr11:46045000-46070600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr11:46045000-46087000	Weak transcription	Hela-S3	cervix
18	chr11:46048000-46070400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr11:46048600-46070600	Weak transcription	Fetal Muscle Leg	muscle
20	chr11:46049200-46071000	Weak transcription	Fetal Brain Male	brain
21	chr11:46049200-46078800	Weak transcription	Aorta	Aorta
22	chr11:46049400-46067200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:46049400-46068400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:46049400-46071000	Weak transcription	HSMM	muscle
25	chr11:46049600-46069200	Weak transcription	HSMMtube	muscle
26	chr11:46053200-46071000	Weak transcription	Gastric	stomach
27	chr11:46055400-46066200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr11:46055400-46070400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:46056400-46067600	Weak transcription	Psoas Muscle	Psoas
30	chr11:46057400-46071000	Weak transcription	NHDF-Ad	bronchial
31	chr11:46059200-46071000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:46060600-46067600	Weak transcription	Left Ventricle	heart
33	chr11:46061600-46068600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr11:46061800-46067200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr11:46061800-46070600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr11:46061800-46070600	Weak transcription	Fetal Stomach	stomach
37	chr11:46062000-46070600	Weak transcription	Colon Smooth Muscle	Colon
38	chr11:46062000-46100800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr11:46062200-46066600	Weak transcription	Ovary	ovary
40	chr11:46062200-46067800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:46062200-46070800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr11:46062200-46071000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr11:46062200-46071000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:46062200-46071000	Weak transcription	Brain Hippocampus Middle	brain
45	chr11:46062200-46071600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr11:46062200-46071800	Weak transcription	Small Intestine	intestine
47	chr11:46062400-46071200	Weak transcription	Osteobl	bone
48	chr11:46062600-46065000	Weak transcription	Fetal Heart	heart
49	chr11:46062600-46065200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr11:46062600-46067200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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