Variant report

Variant	rs12469780
Chromosome Location	chr2:37880619-37880620
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37878873..37880892-chr2:37884421..37886893,2	K562	blood:
2	chr2:37879997..37882658-chr2:37898189..37900305,3	MCF-7	breast:
3	chr2:37869759..37872018-chr2:37878989..37880854,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163171	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12474331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17523989	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3926381	0.88[ASN][1000 genomes]
rs4670746	0.91[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs4670750	0.86[JPT][hapmap]
rs4670758	0.86[AMR][1000 genomes]
rs4670760	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56344180	0.87[ASN][1000 genomes]
rs57048603	0.87[AMR][1000 genomes]
rs59984376	1.00[AFR][1000 genomes]
rs6711909	0.83[JPT][hapmap]
rs6752119	0.83[JPT][hapmap]
rs729793	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv535645	chr2:37853282-37972640	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv535646	chr2:37853282-38014428	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873880	chr2:37868214-37926046	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv535647	chr2:37874563-38014428	Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37853600-37897400	Weak transcription	Small Intestine	intestine
2	chr2:37866800-37881000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:37872000-37892400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr2:37872200-37881800	Weak transcription	Fetal Kidney	kidney
5	chr2:37872400-37880800	Weak transcription	Fetal Brain Male	brain
6	chr2:37873000-37881400	Enhancers	Right Atrium	heart
7	chr2:37873600-37881000	Weak transcription	Ovary	ovary
8	chr2:37873800-37889000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr2:37874200-37881600	Genic enhancers	NHLF	lung
10	chr2:37874400-37881600	Enhancers	Psoas Muscle	Psoas
11	chr2:37874400-37883200	Enhancers	Adipose Nuclei	Adipose
12	chr2:37874600-37884000	Enhancers	Fetal Muscle Leg	muscle
13	chr2:37874600-37893000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:37874800-37882000	Enhancers	Left Ventricle	heart
15	chr2:37875200-37881800	Enhancers	Spleen	Spleen
16	chr2:37875200-37882200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:37875400-37881200	Enhancers	Primary B cells from peripheral blood	blood
18	chr2:37875400-37883400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:37875600-37881000	Weak transcription	Fetal Brain Female	brain
20	chr2:37875600-37881200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:37875800-37881000	Weak transcription	Brain Germinal Matrix	brain
22	chr2:37875800-37881600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:37875800-37882000	Enhancers	Right Ventricle	heart
24	chr2:37875800-37883800	Genic enhancers	NHDF-Ad	bronchial
25	chr2:37875800-37884400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:37875800-37891800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:37875800-37893600	Weak transcription	Fetal Intestine Large	intestine
28	chr2:37875800-37896400	Weak transcription	Fetal Intestine Small	intestine
29	chr2:37876000-37881000	Weak transcription	Fetal Lung	lung
30	chr2:37876000-37881000	Genic enhancers	HSMM	muscle
31	chr2:37876000-37881200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:37876000-37882800	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr2:37876200-37880800	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr2:37876200-37881000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr2:37876200-37881000	Weak transcription	Thymus	Thymus
36	chr2:37876200-37881200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:37876200-37881400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:37876200-37882600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:37876200-37884400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:37877000-37881000	Genic enhancers	HSMMtube	muscle
41	chr2:37877200-37882600	Enhancers	Colon Smooth Muscle	Colon
42	chr2:37877400-37883200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr2:37878000-37881000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr2:37878000-37881800	Genic enhancers	Primary T cells fromperipheralblood	blood
45	chr2:37878000-37886200	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr2:37878200-37881000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:37878400-37881000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr2:37878400-37882000	Enhancers	Primary hematopoietic stem cells	blood
49	chr2:37878400-37882000	Enhancers	Placenta	Placenta
50	chr2:37878400-37894000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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