Variant report

Variant	rs3011782
Chromosome Location	chr10:52290002-52290003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52288714..52291350-chr10:52382116..52385010,2	K562	blood:
2	chr10:52089314..52090958-chr10:52289108..52291926,2	K562	blood:
3	chr10:52120816..52123329-chr10:52287278..52290056,2	MCF-7	breast:
4	chr10:52288714..52294578-chr10:52381112..52386074,5	K562	blood:
5	chr10:52289343..52291383-chr10:52292026..52293996,2	K562	blood:
6	chr10:52289138..52291213-chr10:52296905..52299166,2	K562	blood:
7	chr10:52285415..52288403-chr10:52289940..52291590,2	K562	blood:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10508931	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11006166	0.88[ASN][1000 genomes]
rs11006179	0.88[ASN][1000 genomes]
rs11006183	0.82[ASN][1000 genomes]
rs11006185	0.82[ASN][1000 genomes]
rs11006190	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11006191	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11006193	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11006194	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs11006197	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11006200	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11006213	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11006229	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs11006233	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11006237	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11006238	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1203382	0.90[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs1203386	0.90[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs1203390	0.87[ASN][1000 genomes]
rs1203393	0.90[ASN][1000 genomes]
rs1203394	0.91[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1203395	0.86[ASN][1000 genomes]
rs1203401	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1203403	0.82[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1203405	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1203407	0.91[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1203409	0.91[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1203410	0.90[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1203411	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1203418	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1203420	0.83[ASN][1000 genomes]
rs1203421	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1740761	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17496403	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs17496500	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs1810576	0.90[ASN][1000 genomes]
rs1916567	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2221	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339402	0.82[ASN][1000 genomes]
rs2574985	0.84[JPT][hapmap]
rs2983347	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2983350	0.90[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2983354	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983357	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2983359	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2983361	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2983368	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2983369	0.91[ASN][1000 genomes]
rs2983370	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2983371	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3011770	0.81[CEU][hapmap];0.85[AMR][1000 genomes]
rs3011771	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3011773	0.90[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3011779	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3011780	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3011783	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011786	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3011787	0.95[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3011788	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3011789	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3011790	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3011791	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3011792	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3011793	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3011794	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3011797	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3011801	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7072826	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7921226	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs920136	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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
7	nsv895392	chr10:52263910-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52271600-52300600	Weak transcription	Aorta	Aorta
2	chr10:52272600-52302800	Weak transcription	Fetal Stomach	stomach
3	chr10:52273600-52298400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr10:52273600-52299800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr10:52275200-52294200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr10:52279400-52298200	Weak transcription	Fetal Intestine Small	intestine
7	chr10:52279600-52298400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:52279600-52298400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr10:52279600-52298800	Weak transcription	Lung	lung
10	chr10:52279800-52298600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr10:52282800-52291200	Weak transcription	Esophagus	oesophagus
13	chr10:52282800-52301200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr10:52283000-52300400	Weak transcription	Psoas Muscle	Psoas
15	chr10:52284400-52292400	Weak transcription	Brain Angular Gyrus	brain
16	chr10:52284600-52297600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:52285400-52293200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr10:52286200-52291400	Weak transcription	Gastric	stomach
19	chr10:52286400-52304000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr10:52287000-52290200	Enhancers	Brain Substantia Nigra	brain
21	chr10:52287400-52298200	Weak transcription	Left Ventricle	heart
22	chr10:52287600-52291200	Weak transcription	Pancreas	Pancrea
23	chr10:52287600-52291600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr10:52287600-52292000	Weak transcription	Stomach Mucosa	stomach
25	chr10:52287600-52294000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr10:52287600-52296800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr10:52287600-52296800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr10:52287800-52302800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr10:52288200-52298600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr10:52288400-52290800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr10:52288400-52291600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr10:52288600-52291200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr10:52288600-52300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:52288800-52291200	Weak transcription	K562	blood
35	chr10:52288800-52291800	Weak transcription	Fetal Heart	heart
36	chr10:52289400-52300000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr10:52289600-52290200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr10:52290000-52294400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr10:52290000-52295800	Weak transcription	Brain Hippocampus Middle	brain
40	chr10:52290000-52296000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr10:52290000-52296600	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links