Variant report

Variant	rs11005956
Chromosome Location	chr10:52262328-52262329
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52260554..52263861-chr10:52272806..52275340,3	K562	blood:
2	chr10:52261680..52263393-chr10:52269137..52270888,2	MCF-7	breast:
3	chr10:52261590..52264231-chr10:52382016..52385854,3	MCF-7	breast:
4	chr10:52260913..52263202-chr10:52364630..52366882,2	MCF-7	breast:
5	chr10:52260323..52263504-chr10:52265636..52267832,3	MCF-7	breast:
6	chr10:52230115..52234351-chr10:52258743..52262560,5	MCF-7	breast:
7	chr10:52230142..52232797-chr10:52261125..52263960,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230036	Chromatin interaction
ENSG00000198964	Chromatin interaction
ENSG00000225303	Chromatin interaction
ENSG00000226200	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10443954	1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508926	1.00[CHB][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508930	0.91[YRI][hapmap]
rs10740666	1.00[CHB][hapmap]
rs10763560	0.83[YRI][hapmap]
rs10825903	0.92[TSI][hapmap]
rs10826032	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826101	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005316	1.00[ASN][1000 genomes]
rs11005345	1.00[CHB][hapmap];0.83[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	0.80[EUR][1000 genomes]
rs11005708	1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005730	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs11005872	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]
rs11005877	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005882	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005952	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006012	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11516712	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11591645	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11595661	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598794	1.00[ASN][1000 genomes]
rs12354779	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12355439	1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12356013	1.00[CHB][hapmap]
rs12357733	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358247	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]
rs12360058	1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.83[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	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58969905	1.00[ASN][1000 genomes]
rs61739586	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071001	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078586	1.00[ASN][1000 genomes]
rs7078940	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082728	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7091881	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096968	0.99[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	0.80[EUR][1000 genomes]
rs74132723	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7477280	1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908093	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv895391	chr10:52260398-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11005956	FRMPD2	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52247000-52271200	Weak transcription	Colon Smooth Muscle	Colon
2	chr10:52249200-52266800	Weak transcription	Primary B cells from cord blood	blood
3	chr10:52253800-52268200	Weak transcription	Fetal Intestine Small	intestine
4	chr10:52255000-52267200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:52255400-52266600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr10:52256600-52263000	Weak transcription	Right Ventricle	heart
7	chr10:52258000-52266600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr10:52258000-52266600	Weak transcription	Ovary	ovary
9	chr10:52258000-52267200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr10:52258000-52271800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr10:52260400-52263600	Enhancers	Brain Substantia Nigra	brain
12	chr10:52260600-52264000	Enhancers	Brain Angular Gyrus	brain
13	chr10:52260600-52264000	Enhancers	HepG2	liver
14	chr10:52260800-52262400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:52260800-52262400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr10:52260800-52262400	Enhancers	Stomach Mucosa	stomach
17	chr10:52260800-52262400	Enhancers	NHEK	skin
18	chr10:52260800-52264400	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr10:52260800-52264600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr10:52260800-52264600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr10:52260800-52264600	Enhancers	Brain Cingulate Gyrus	brain
22	chr10:52261000-52262400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr10:52261000-52268200	Weak transcription	Gastric	stomach
24	chr10:52261200-52264000	Enhancers	Brain Anterior Caudate	brain
25	chr10:52261400-52262400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr10:52261400-52262400	Enhancers	HMEC	breast
27	chr10:52261400-52262800	Enhancers	K562	blood
28	chr10:52261400-52263800	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr10:52261400-52264000	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr10:52261400-52264400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr10:52261400-52266600	Weak transcription	Fetal Lung	lung
32	chr10:52261600-52262400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr10:52261600-52262400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:52261600-52262400	Enhancers	Placenta	Placenta
35	chr10:52261600-52262400	Enhancers	Fetal Stomach	stomach
36	chr10:52261600-52262400	Flanking Active TSS	GM12878-XiMat	blood
37	chr10:52261600-52262400	Enhancers	Hela-S3	cervix
38	chr10:52261600-52262600	Enhancers	Fetal Intestine Large	intestine
39	chr10:52261600-52263600	Enhancers	Primary T cells fromperipheralblood	blood
40	chr10:52261600-52264200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr10:52261600-52264200	Enhancers	Fetal Heart	heart
42	chr10:52261600-52264400	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr10:52261600-52264600	Enhancers	Brain Hippocampus Middle	brain
44	chr10:52261800-52262400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr10:52261800-52262400	Enhancers	Primary T cells from cord blood	blood
46	chr10:52261800-52262400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr10:52261800-52262400	Enhancers	Esophagus	oesophagus
48	chr10:52261800-52262400	Enhancers	Left Ventricle	heart
49	chr10:52261800-52262400	Enhancers	Right Atrium	heart
50	chr10:52261800-52262400	Enhancers	A549	lung

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