Variant report

Variant	rs8848
Chromosome Location	chr11:76262652-76262653
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:76262469..76263152-chr11:76392001..76392517,2	K562	blood:
2	chr11:76261079..76263436-chr11:76264364..76265867,2	K562	blood:
3	chr11:76262380..76263432-chr11:76391914..76393026,4	MCF-7	breast:
4	chr11:76262034..76262940-chr11:76309241..76310049,2	K562	blood:
5	chr11:76250200..76253023-chr11:76260666..76263366,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10160382	0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1044265	0.93[ASW][hapmap]
rs10793167	0.81[CEU][hapmap];0.83[YRI][hapmap]
rs10793169	0.93[ASW][hapmap];0.92[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs10793171	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[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];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899227	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11606394	0.93[ASW][hapmap]
rs17749618	0.85[CEU][hapmap]
rs1939467	0.81[CEU][hapmap]
rs1939468	0.85[CEU][hapmap]
rs2508740	0.87[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2508741	0.87[ASW][hapmap];0.96[CEU][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2508753	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2508756	0.93[ASW][hapmap]
rs2508759	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2508760	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2508761	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[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];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2508762	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2513504	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2513505	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2513508	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2513513	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2513520	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2513523	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2513525	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3753051	0.85[CEU][hapmap]
rs3814711	0.92[CEU][hapmap]
rs4245443	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4272809	0.93[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs4300410	0.93[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs4945087	0.80[ASW][hapmap]
rs4945090	0.96[CEU][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes]
rs5023625	0.80[AMR][1000 genomes]
rs55977477	0.86[EUR][1000 genomes]
rs7106564	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7107058	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap]
rs7123361	0.85[CEU][hapmap]
rs7125552	0.81[CEU][hapmap]
rs7926009	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs7949258	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050713	chr11:76147085-76267117	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1848387	chr11:76243699-76262652	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8848	ARHGEF17	cis	cerebellum	SCAN
rs8848	ALG8	cis	cerebellum	SCAN
rs8848	ARRB1	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76224400-76263800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:76230000-76265600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:76233800-76263200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:76234800-76263000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:76252600-76263000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:76254800-76265800	Weak transcription	Fetal Heart	heart
7	chr11:76254800-76269800	Weak transcription	NHDF-Ad	bronchial
8	chr11:76255200-76265200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:76255800-76263200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:76256000-76264800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:76256000-76265400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:76256000-76266400	Weak transcription	A549	lung
13	chr11:76256000-76273400	Weak transcription	Psoas Muscle	Psoas
14	chr11:76256200-76265800	Weak transcription	Colonic Mucosa	Colon
15	chr11:76256200-76265800	Weak transcription	Fetal Brain Male	brain
16	chr11:76257200-76266400	Weak transcription	Brain Angular Gyrus	brain
17	chr11:76257200-76266600	Weak transcription	Small Intestine	intestine
18	chr11:76257200-76270200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:76257200-76272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:76257400-76262800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr11:76257400-76263000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:76257400-76263400	Weak transcription	Pancreas	Pancrea
23	chr11:76257400-76263800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr11:76257400-76264000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:76257400-76264400	Weak transcription	Fetal Intestine Small	intestine
26	chr11:76257400-76264600	Weak transcription	Fetal Stomach	stomach
27	chr11:76257400-76264800	Weak transcription	Colon Smooth Muscle	Colon
28	chr11:76257400-76265600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr11:76257400-76265800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr11:76257400-76267800	Weak transcription	Esophagus	oesophagus
31	chr11:76257400-76269800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr11:76257400-76269800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:76257400-76270600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:76257400-76270800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr11:76257400-76271000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:76257400-76271000	Weak transcription	HSMMtube	muscle
37	chr11:76257400-76271000	Weak transcription	NHEK	skin
38	chr11:76257400-76271800	Weak transcription	Lung	lung
39	chr11:76257400-76272200	Weak transcription	Spleen	Spleen
40	chr11:76257400-76272400	Weak transcription	Ovary	ovary
41	chr11:76257600-76263800	Weak transcription	Right Ventricle	heart
42	chr11:76257600-76265200	Weak transcription	Fetal Kidney	kidney
43	chr11:76257800-76263200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:76257800-76264800	Weak transcription	Fetal Intestine Large	intestine
45	chr11:76257800-76271400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr11:76258000-76263400	Weak transcription	HepG2	liver
47	chr11:76258000-76270600	Weak transcription	Brain Substantia Nigra	brain
48	chr11:76258200-76264400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr11:76258200-76270600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:76258400-76266600	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links