Variant report

Variant	rs12358247
Chromosome Location	chr10:52121679-52121680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52115339..52118767-chr10:52119079..52123600,6	K562	blood:
2	chr10:52120330..52124092-chr10:52125493..52129232,4	K562	blood:
3	chr10:52120816..52123329-chr10:52287278..52290056,2	MCF-7	breast:
4	chr10:52084925..52086838-chr10:52120229..52123147,2	K562	blood:
5	chr10:52115339..52118395-chr10:52119759..52122908,4	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10443954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508929	0.93[YRI][hapmap]
rs10740666	1.00[CHB][hapmap]
rs10825903	0.87[CEU][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10826032	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826101	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005316	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005345	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005502	1.00[CHB][hapmap]
rs11005595	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005612	0.87[EUR][1000 genomes]
rs11005708	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs11005872	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]
rs11005877	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005882	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005952	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005956	1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006012	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11516712	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11591645	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11595661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598794	1.00[ASN][1000 genomes]
rs12354779	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12355439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12356013	1.00[CHB][hapmap]
rs12357733	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360058	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177372	1.00[ASN][1000 genomes]
rs56251625	1.00[ASN][1000 genomes]
rs57959812	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58969905	1.00[ASN][1000 genomes]
rs61739586	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071001	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078940	0.93[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082728	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7091881	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096968	1.00[CEU][hapmap];0.84[EUR][1000 genomes];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	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74132723	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7477280	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518071	chr10:51595893-52157935	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	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
3	nsv1053903	chr10:51886486-52163991	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1040661	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1051028	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1037118	chr10:51886486-52167442	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	esv2830205	chr10:51978430-52135215	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv1046850	chr10:52009869-52135542	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv540625	chr10:52009869-52135542	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
15	nsv430231	chr10:52119046-52163531	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12358247	FRMPD2	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52096400-52123000	Weak transcription	Small Intestine	intestine
2	chr10:52103000-52122400	Weak transcription	HUVEC	blood vessel
3	chr10:52104000-52123200	Weak transcription	Aorta	Aorta
4	chr10:52104000-52134000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr10:52104000-52141400	Weak transcription	Pancreas	Pancrea
6	chr10:52104200-52133600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr10:52104200-52134200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr10:52104200-52157000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr10:52108000-52125400	Weak transcription	Right Ventricle	heart
10	chr10:52109400-52134400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr10:52111800-52123000	Weak transcription	Primary T cells from cord blood	blood
12	chr10:52115800-52142200	Weak transcription	Fetal Intestine Small	intestine
13	chr10:52117400-52133400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr10:52117600-52121800	Enhancers	Brain Cingulate Gyrus	brain
15	chr10:52117600-52122200	Enhancers	Fetal Lung	lung
16	chr10:52118200-52121800	Enhancers	Adipose Nuclei	Adipose
17	chr10:52118800-52121800	Enhancers	Liver	Liver
18	chr10:52119000-52121800	Enhancers	Fetal Kidney	kidney
19	chr10:52119000-52129400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:52119000-52133200	Weak transcription	Colon Smooth Muscle	Colon
21	chr10:52119400-52127400	Weak transcription	Hela-S3	cervix
22	chr10:52119400-52134000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:52119400-52136000	Weak transcription	Fetal Brain Male	brain
24	chr10:52119800-52125400	Genic enhancers	K562	blood
25	chr10:52120000-52122200	Enhancers	NHDF-Ad	bronchial
26	chr10:52120200-52121800	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr10:52120200-52121800	Enhancers	Right Atrium	heart
28	chr10:52120200-52122000	Enhancers	Brain Anterior Caudate	brain
29	chr10:52120400-52121800	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr10:52120400-52121800	Enhancers	Brain Substantia Nigra	brain
31	chr10:52120400-52121800	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr10:52120400-52133000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr10:52120600-52121800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr10:52120600-52121800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr10:52120600-52122400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
36	chr10:52120600-52133800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr10:52120600-52141400	Weak transcription	HSMM	muscle
38	chr10:52120800-52121800	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr10:52120800-52121800	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr10:52120800-52122400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr10:52120800-52124200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:52120800-52133000	Weak transcription	HSMMtube	muscle
43	chr10:52120800-52133400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr10:52120800-52133600	Weak transcription	Osteobl	bone
45	chr10:52121000-52121800	Genic enhancers	Primary B cells from cord blood	blood
46	chr10:52121000-52122200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr10:52121200-52121800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr10:52121200-52124400	Weak transcription	Fetal Heart	heart
49	chr10:52121200-52127000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr10:52121200-52134400	Weak transcription	Fetal Stomach	stomach

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