Variant report

Variant	rs11005872
Chromosome Location	chr10:52239232-52239233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10443954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10740666	1.00[CHB][hapmap]
rs10825903	0.87[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs10826032	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826101	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005316	1.00[ASN][1000 genomes]
rs11005345	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005502	1.00[CHB][hapmap]
rs11005595	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005612	0.81[EUR][1000 genomes]
rs11005708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11005877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005882	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005952	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005956	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006012	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11516712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11591645	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11595661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598794	1.00[ASN][1000 genomes]
rs12354779	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12355439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12356013	1.00[CHB][hapmap]
rs12357733	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17581623	1.00[CHB][hapmap]
rs2177372	1.00[ASN][1000 genomes]
rs3001855	1.00[ASN][1000 genomes]
rs3001884	1.00[ASN][1000 genomes]
rs56251625	1.00[ASN][1000 genomes]
rs57959812	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58969905	1.00[ASN][1000 genomes]
rs61739586	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071001	0.93[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078586	1.00[ASN][1000 genomes]
rs7078940	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082728	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7091881	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096968	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099535	1.00[ASN][1000 genomes]
rs72787008	1.00[ASN][1000 genomes]
rs72803755	1.00[ASN][1000 genomes]
rs74131268	1.00[ASN][1000 genomes]
rs74131270	1.00[ASN][1000 genomes]
rs74131283	1.00[ASN][1000 genomes]
rs74131284	1.00[ASN][1000 genomes]
rs74132707	0.81[EUR][1000 genomes]
rs74132723	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7477280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908093	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11005872	FRMPD2	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52208000-52240200	Weak transcription	Esophagus	oesophagus
2	chr10:52218000-52240200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:52220000-52243600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr10:52229800-52242600	Weak transcription	Thymus	Thymus
5	chr10:52229800-52244000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr10:52229800-52252000	Weak transcription	Aorta	Aorta
7	chr10:52230000-52240000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr10:52230400-52240000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr10:52230600-52256400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr10:52231000-52239400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr10:52231200-52240000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr10:52231200-52240200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr10:52231200-52242000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr10:52231200-52244600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr10:52231200-52257800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr10:52231800-52243000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr10:52232400-52242400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr10:52234000-52240200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr10:52234000-52240200	Weak transcription	Gastric	stomach
20	chr10:52234000-52240200	Weak transcription	Right Ventricle	heart
21	chr10:52234000-52242200	Weak transcription	Psoas Muscle	Psoas
22	chr10:52234000-52243600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr10:52234000-52261600	Weak transcription	Pancreas	Pancrea
24	chr10:52234200-52246800	Weak transcription	Brain Anterior Caudate	brain
25	chr10:52235200-52243200	Weak transcription	Brain Hippocampus Middle	brain
26	chr10:52236000-52240400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr10:52237000-52240200	Weak transcription	Fetal Stomach	stomach
28	chr10:52237000-52240600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr10:52237000-52240800	Weak transcription	Fetal Lung	lung
30	chr10:52237000-52242200	Weak transcription	K562	blood
31	chr10:52237000-52243200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr10:52237000-52250400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr10:52237200-52243200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr10:52237400-52240800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr10:52237400-52242200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr10:52237600-52240200	Weak transcription	Lung	lung
37	chr10:52237600-52240400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr10:52237600-52240600	Strong transcription	Primary B cells from cord blood	blood
39	chr10:52237800-52240200	Weak transcription	Fetal Intestine Small	intestine
40	chr10:52237800-52255000	Weak transcription	Liver	Liver
41	chr10:52237800-52261800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr10:52238000-52239800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr10:52238800-52243400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr10:52239200-52240000	Weak transcription	Primary T cells from cord blood	blood
45	chr10:52239200-52240000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr10:52239200-52241000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr10:52239200-52243600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links