Variant report

Variant	rs4752843
Chromosome Location	chr11:47531884-47531885
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47530411..47532334-chr11:47573326..47575672,2	K562	blood:
2	chr11:47531749..47534788-chr11:47570653..47573178,3	K562	blood:
3	chr11:47531412..47534315-chr11:47879046..47881492,2	K562	blood:

Variant related genes	Relation type
ENSG00000149187	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1044269	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10742805	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs10742806	0.94[JPT][hapmap]
rs10742816	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs10769255	0.82[CEU][hapmap]
rs11039278	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11819955	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11820650	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11821273	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11821860	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11821917	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes]
rs11822402	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11823490	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11824864	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes]
rs11824971	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11824990	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11828339	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap]
rs12419342	0.94[JPT][hapmap]
rs1474056	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs17198158	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17790804	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17791016	0.92[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap]
rs2138767	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs2242511	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3740684	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs3781628	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3824867	0.88[GIH][hapmap];0.94[JPT][hapmap]
rs3847503	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4147730	1.00[ASW][hapmap];0.91[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]
rs4237544	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs4282946	0.94[JPT][hapmap]
rs4384349	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4752783	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4752786	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs4752829	0.88[JPT][hapmap]
rs4752837	0.94[JPT][hapmap]
rs4752839	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4752842	0.82[MEX][hapmap]
rs59631865	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60882887	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60929305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61000762	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7105122	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs7105907	0.94[JPT][hapmap]
rs7111873	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs7115371	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7120737	0.92[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs7126210	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs753812	0.85[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7931089	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7939069	0.92[ASW][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];0.84[YRI][hapmap]
rs7948705	0.94[JPT][hapmap]
rs7952204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9666924	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4752843	ATG13	cis	parietal	SCAN
rs4752843	SLC35C1	cis	cerebellum	SCAN
rs4752843	TTC17	cis	cerebellum	SCAN
rs4752843	LOC441601	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47509000-47534400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:47510200-47536800	Weak transcription	Fetal Kidney	kidney
3	chr11:47521600-47534000	Weak transcription	Aorta	Aorta
4	chr11:47521600-47534400	Weak transcription	HUVEC	blood vessel
5	chr11:47522800-47536200	Weak transcription	Fetal Brain Female	brain
6	chr11:47523000-47536600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:47523000-47545600	Weak transcription	Dnd41	blood
8	chr11:47524800-47549600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:47526400-47533400	Weak transcription	Fetal Stomach	stomach
10	chr11:47528000-47532000	Enhancers	HSMM	muscle
11	chr11:47528000-47532400	Enhancers	Stomach Mucosa	stomach
12	chr11:47528000-47535000	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr11:47528000-47538200	Enhancers	Osteobl	bone
14	chr11:47528200-47532000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr11:47528200-47532000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr11:47528200-47532200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:47528200-47532200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr11:47528200-47532400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr11:47528400-47532000	Enhancers	Brain Angular Gyrus	brain
20	chr11:47528400-47532000	Enhancers	Brain Anterior Caudate	brain
21	chr11:47528400-47532200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr11:47528400-47532600	Enhancers	Liver	Liver
23	chr11:47528400-47533400	Enhancers	Primary T cells from cord blood	blood
24	chr11:47528400-47536400	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr11:47528400-47536800	Enhancers	Primary B cells from peripheral blood	blood
26	chr11:47528400-47544800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr11:47528800-47536600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:47528800-47541000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr11:47529000-47534400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr11:47529200-47532000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr11:47529200-47532000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr11:47529200-47532200	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr11:47529200-47534400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr11:47529200-47535000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:47529200-47536400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr11:47529200-47536600	Weak transcription	Brain Germinal Matrix	brain
37	chr11:47529400-47532000	Enhancers	Fetal Intestine Large	intestine
38	chr11:47529400-47533800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:47529600-47532000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:47529800-47532200	Enhancers	Gastric	stomach
41	chr11:47529800-47534000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:47529800-47534200	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr11:47529800-47534400	Weak transcription	Fetal Heart	heart
44	chr11:47529800-47534600	Enhancers	Psoas Muscle	Psoas
45	chr11:47530000-47534200	Weak transcription	Fetal Lung	lung
46	chr11:47530200-47532000	Enhancers	Left Ventricle	heart
47	chr11:47530200-47532000	Enhancers	Right Ventricle	heart
48	chr11:47530200-47532200	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr11:47530200-47543000	Enhancers	Primary T cells fromperipheralblood	blood
50	chr11:47530400-47532000	Enhancers	HUES48 Cell Line	embryonic stem cell

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