Variant report

Variant	rs56234858
Chromosome Location	chr11:62272240-62272241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:62205267..62207782-chr11:62271723..62274072,2	K562	blood:
2	chr11:62270607..62282151-chr11:62305075..62317987,34	MCF-7	breast:
3	chr11:62271795..62272366-chr11:62309145..62309964,2	MCF-7	breast:
4	chr11:62271698..62273633-chr11:62313445..62315600,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124942	Chromatin interaction
ENSG00000257058	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10897285	0.91[ASN][1000 genomes]
rs11231108	0.91[ASN][1000 genomes]
rs11231109	0.91[ASN][1000 genomes]
rs11231110	0.91[ASN][1000 genomes]
rs11231111	0.91[ASN][1000 genomes]
rs11231112	0.82[ASN][1000 genomes]
rs11231115	0.91[ASN][1000 genomes]
rs11231116	0.91[ASN][1000 genomes]
rs11231117	0.91[ASN][1000 genomes]
rs11231119	0.91[ASN][1000 genomes]
rs11231120	0.91[ASN][1000 genomes]
rs11231121	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11231128	0.81[EUR][1000 genomes]
rs11231130	0.81[EUR][1000 genomes]
rs11819950	0.91[ASN][1000 genomes]
rs11822224	0.91[ASN][1000 genomes]
rs11826756	0.91[ASN][1000 genomes]
rs11827029	0.91[ASN][1000 genomes]
rs12223424	0.91[ASN][1000 genomes]
rs12271287	0.91[ASN][1000 genomes]
rs12273682	0.91[ASN][1000 genomes]
rs12273757	0.91[ASN][1000 genomes]
rs12273761	0.91[ASN][1000 genomes]
rs12281588	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12281651	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12289932	0.91[ASN][1000 genomes]
rs12291022	0.91[ASN][1000 genomes]
rs12291805	0.81[EUR][1000 genomes]
rs12292433	0.81[EUR][1000 genomes]
rs12294680	0.91[ASN][1000 genomes]
rs17157332	0.91[ASN][1000 genomes]
rs17157338	0.91[ASN][1000 genomes]
rs17157363	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17157365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35117866	0.91[ASN][1000 genomes]
rs3867144	0.91[ASN][1000 genomes]
rs4124	0.91[ASN][1000 genomes]
rs56973213	0.91[ASN][1000 genomes]
rs57973105	0.91[ASN][1000 genomes]
rs59295893	0.91[ASN][1000 genomes]
rs61312994	0.81[EUR][1000 genomes]
rs61625484	0.81[EUR][1000 genomes]
rs7105793	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7108380	0.85[EUR][1000 genomes]
rs7123692	0.81[EUR][1000 genomes]
rs7124044	0.82[ASN][1000 genomes]
rs7124130	0.81[EUR][1000 genomes]
rs7127582	0.90[EUR][1000 genomes]
rs73500219	0.91[ASN][1000 genomes]
rs7929818	0.91[ASN][1000 genomes]
rs7937521	0.85[EUR][1000 genomes]
rs7946258	0.91[ASN][1000 genomes]
rs7951639	0.81[EUR][1000 genomes];0.82[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	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	nsv897621	chr11:62230309-62290170	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	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

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62247800-62272600	Weak transcription	Aorta	Aorta
2	chr11:62265400-62272400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr11:62266400-62272800	Enhancers	Placenta	Placenta
4	chr11:62267000-62277400	Enhancers	Fetal Heart	heart
5	chr11:62267600-62275600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr11:62267800-62272600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr11:62267800-62272800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:62268000-62274600	Weak transcription	Hela-S3	cervix
9	chr11:62268400-62272600	Weak transcription	Osteobl	bone
10	chr11:62268600-62272600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:62268600-62272800	Weak transcription	NHEK	skin
12	chr11:62269400-62272400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:62269400-62272800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:62269400-62275800	Weak transcription	HMEC	breast
15	chr11:62269600-62272400	Enhancers	K562	blood
16	chr11:62269600-62272600	Enhancers	Stomach Smooth Muscle	stomach
17	chr11:62269600-62273800	Weak transcription	Gastric	stomach
18	chr11:62269600-62275400	Weak transcription	Pancreas	Pancrea
19	chr11:62269800-62272400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:62269800-62272400	Weak transcription	NHDF-Ad	bronchial
21	chr11:62269800-62272800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:62269800-62275800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:62270000-62272400	Weak transcription	Brain Angular Gyrus	brain
24	chr11:62270200-62272400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:62270200-62272600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:62270200-62272600	Weak transcription	Esophagus	oesophagus
27	chr11:62270400-62272400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:62270400-62272400	Weak transcription	Fetal Lung	lung
29	chr11:62270400-62272600	Weak transcription	Right Atrium	heart
30	chr11:62270400-62272800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr11:62270600-62272400	Weak transcription	Stomach Mucosa	stomach
32	chr11:62270800-62272400	Weak transcription	Fetal Intestine Small	intestine
33	chr11:62270800-62272400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr11:62270800-62272600	Weak transcription	Brain Hippocampus Middle	brain
35	chr11:62270800-62272800	Weak transcription	HUVEC	blood vessel
36	chr11:62270800-62275800	Weak transcription	Psoas Muscle	Psoas
37	chr11:62270800-62281600	Weak transcription	Liver	Liver
38	chr11:62271000-62272600	Weak transcription	Spleen	Spleen
39	chr11:62271000-62273000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:62271000-62276200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr11:62271200-62272400	Weak transcription	Adipose Nuclei	Adipose
42	chr11:62271200-62275600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr11:62271200-62275600	Enhancers	Placenta Amnion	Placenta Amnion
44	chr11:62271200-62275800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr11:62271400-62272400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr11:62271400-62272800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr11:62271400-62275600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr11:62271400-62275600	Enhancers	A549	lung
49	chr11:62271600-62273600	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr11:62271800-62272400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links