Variant report

Variant	rs71490390
Chromosome Location	chr11:62329185-62329186
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62328062..62329768-chr11:62438392..62441181,2	K562	blood:
2	chr11:62326831..62332617-chr11:62337718..62342722,6	MCF-7	breast:
3	chr11:62326922..62329969-chr11:62332380..62335184,3	MCF-7	breast:
4	chr11:62328251..62329774-chr11:62605498..62607870,2	MCF-7	breast:
5	chr11:62319256..62325692-chr11:62326835..62334390,9	K562	blood:
6	chr11:62326979..62329934-chr11:62331462..62336636,5	K562	blood:
7	chr11:62328044..62331009-chr11:62411420..62414056,2	MCF-7	breast:
8	chr11:62275811..62278092-chr11:62326912..62329535,2	MCF-7	breast:
9	chr11:62328251..62330018-chr11:62332722..62335121,2	MCF-7	breast:
10	chr11:62326681..62329872-chr11:62430433..62433667,3	MCF-7	breast:
11	chr11:62328388..62330000-chr11:62343095..62344668,2	K562	blood:
12	chr11:62328250..62330762-chr11:62331688..62334513,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000214756	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000124942	Chromatin interaction
ENSG00000254772	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1061093	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231137	0.97[ASN][1000 genomes]
rs11231138	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11231141	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231144	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231145	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231150	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11231151	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11231152	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11231154	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11231155	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11231156	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11231161	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11553576	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12049914	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12223627	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12225213	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12226821	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12808829	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17773169	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1801144	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2428548	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2428549	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2428551	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2509961	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2509967	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2509982	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2512562	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2512563	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2516634	0.88[EUR][1000 genomes]
rs2849030	0.86[EUR][1000 genomes]
rs2849031	0.88[EUR][1000 genomes]
rs34065644	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34894392	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35587183	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35880596	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58720921	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60098285	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61296092	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7124057	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71490392	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71490394	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72927213	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7928833	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930896	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7937146	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7942154	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7942991	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7943191	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv832180	chr11:62201605-62364828	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
5	esv3584599	chr11:62262742-62398050	Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	esv1801128	chr11:62276347-62329897	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
7	esv1831183	chr11:62276347-62329897	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
8	nsv832182	chr11:62295575-62462848	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
9	nsv347	chr11:62297068-62338927	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
10	nsv825939	chr11:62326083-62410577	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS 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 miRNA target site	122 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs71490390	MTA2	cis	Esophagus Mucosa	GTEx
rs71490390	EML3	cis	Whole Blood	GTEx
rs71490390	ROM1	cis	Thyroid	GTEx
rs71490390	EML3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62322400-62340000	Strong transcription	Fetal Brain Female	brain
2	chr11:62322600-62331200	Weak transcription	Ovary	ovary
3	chr11:62324600-62331600	Genic enhancers	Placenta	Placenta
4	chr11:62324800-62329600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr11:62324800-62330000	Genic enhancers	HMEC	breast
6	chr11:62324800-62333600	Weak transcription	Small Intestine	intestine
7	chr11:62324800-62338800	Strong transcription	Brain Germinal Matrix	brain
8	chr11:62324800-62339600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:62325000-62331200	Weak transcription	Psoas Muscle	Psoas
10	chr11:62325000-62331800	Genic enhancers	A549	lung
11	chr11:62325000-62338600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:62325000-62338800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:62325200-62329800	Strong transcription	Thymus	Thymus
14	chr11:62325200-62339600	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr11:62325600-62329400	Strong transcription	Brain Cingulate Gyrus	brain
16	chr11:62325800-62329200	Genic enhancers	Rectal Mucosa Donor 29	rectum
17	chr11:62326000-62329800	Genic enhancers	HUVEC	blood vessel
18	chr11:62326000-62330000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:62326200-62329400	Genic enhancers	K562	blood
20	chr11:62326200-62329400	Genic enhancers	NH-A	brain
21	chr11:62326200-62330400	Strong transcription	Fetal Kidney	kidney
22	chr11:62326400-62330200	Strong transcription	Primary T cells from cord blood	blood
23	chr11:62326400-62339200	Strong transcription	Fetal Thymus	thymus
24	chr11:62326800-62337400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr11:62327200-62329800	Genic enhancers	Muscle Satellite Cultured Cells	--
26	chr11:62327400-62330000	Genic enhancers	Fetal Intestine Small	intestine
27	chr11:62327600-62329400	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr11:62327600-62330000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr11:62327600-62331800	Weak transcription	Aorta	Aorta
30	chr11:62327600-62331800	Genic enhancers	Fetal Intestine Large	intestine
31	chr11:62327600-62333200	Weak transcription	Pancreas	Pancrea
32	chr11:62327800-62329400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:62327800-62329800	Weak transcription	Lung	lung
34	chr11:62327800-62330000	Weak transcription	Brain Substantia Nigra	brain
35	chr11:62327800-62330800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:62327800-62330800	Weak transcription	Primary B cells from cord blood	blood
37	chr11:62327800-62330800	Weak transcription	Esophagus	oesophagus
38	chr11:62327800-62330800	Weak transcription	Left Ventricle	heart
39	chr11:62328000-62329800	Enhancers	HepG2	liver
40	chr11:62328000-62330400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:62328200-62329400	Enhancers	HSMM	muscle
42	chr11:62328400-62329200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:62328400-62329800	Strong transcription	Fetal Lung	lung
44	chr11:62328400-62330200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr11:62328400-62330400	Weak transcription	Brain Angular Gyrus	brain
46	chr11:62328400-62331000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:62328400-62331000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr11:62328400-62331000	Weak transcription	Right Atrium	heart
49	chr11:62328400-62331200	Weak transcription	Colonic Mucosa	Colon
50	chr11:62328400-62333200	Weak transcription	Gastric	stomach

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