Variant report

Variant	rs12580599
Chromosome Location	chr12:51702914-51702915
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51701016..51703258-chr12:51704233..51707521,3	MCF-7	breast:
2	chr12:51702787..51706135-chr12:51715860..51718375,3	K562	blood:
3	chr12:51696998..51699958-chr12:51701711..51703812,2	K562	blood:

Variant related genes	Relation type
ENSG00000110934	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10783431	0.96[CEU][hapmap];0.98[TSI][hapmap]
rs11169800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169806	0.96[CEU][hapmap]
rs11612245	0.96[CEU][hapmap]
rs12580302	0.81[ASN][1000 genomes]
rs12814917	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12816187	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs2006749	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs3847862	0.96[CEU][hapmap];0.98[TSI][hapmap]
rs4335588	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56869579	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57484374	0.83[ASN][1000 genomes]
rs58673573	0.80[ASN][1000 genomes]
rs61172662	0.85[ASN][1000 genomes]
rs61605107	0.80[ASN][1000 genomes]
rs7301933	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7309232	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7312857	0.83[CHB][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];0.90[YRI][hapmap];0.80[ASN][1000 genomes]
rs7316301	0.80[ASN][1000 genomes]
rs74093823	0.85[ASN][1000 genomes]
rs74093827	0.85[ASN][1000 genomes]
rs7975534	0.83[EUR][1000 genomes]
rs934089	0.96[CEU][hapmap];0.98[TSI][hapmap]
rs9652000	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong 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	21 gene(s)	inside rSNPs	diseases
2	nsv469377	chr12:51690751-51733951	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv558877	chr12:51690751-51733951	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12580599	DNAJC22	cis	parietal	SCAN
rs12580599	COL2A1	cis	parietal	SCAN
rs12580599	ELA1	cis	multi-tissue	Pritchard

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51674200-51704000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:51681800-51714200	Weak transcription	Gastric	stomach
3	chr12:51687000-51703800	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:51687000-51707400	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr12:51687800-51708000	Strong transcription	Thymus	Thymus
6	chr12:51696600-51712400	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr12:51698400-51712600	Weak transcription	Spleen	Spleen
8	chr12:51699200-51709400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
9	chr12:51699800-51710000	Strong transcription	Fetal Thymus	thymus
10	chr12:51700600-51703000	Weak transcription	Esophagus	oesophagus
11	chr12:51700600-51711000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr12:51700800-51703000	Weak transcription	Primary B cells from cord blood	blood
13	chr12:51701200-51704000	Enhancers	Stomach Mucosa	stomach
14	chr12:51701400-51703000	Enhancers	Fetal Intestine Small	intestine
15	chr12:51701400-51703000	Flanking Active TSS	A549	lung
16	chr12:51701400-51703000	Enhancers	Osteobl	bone
17	chr12:51701400-51704000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:51701400-51704800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr12:51701400-51706800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr12:51701400-51708600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:51701600-51703000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:51701600-51703000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:51701600-51703000	Enhancers	Fetal Intestine Large	intestine
24	chr12:51701600-51703000	Flanking Active TSS	Hela-S3	cervix
25	chr12:51701600-51703000	Enhancers	HMEC	breast
26	chr12:51701600-51703000	Enhancers	NHDF-Ad	bronchial
27	chr12:51701600-51703200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:51701600-51706400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr12:51701600-51706600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:51701600-51708400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
31	chr12:51701800-51703000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:51701800-51703000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:51701800-51703200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:51702000-51703000	Weak transcription	Small Intestine	intestine
35	chr12:51702000-51705400	Strong transcription	Primary hematopoietic stem cells	blood
36	chr12:51702200-51703000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr12:51702200-51703000	Active TSS	Rectal Smooth Muscle	rectum
38	chr12:51702200-51703400	Strong transcription	Placenta	Placenta
39	chr12:51702200-51703600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:51702200-51712400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:51702400-51703000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:51702400-51703000	Enhancers	NH-A	brain
43	chr12:51702400-51703200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:51702400-51703200	Strong transcription	Primary T cells from cord blood	blood
45	chr12:51702400-51703400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:51702400-51704200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr12:51702400-51705800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr12:51702400-51705800	Weak transcription	Pancreas	Pancrea
49	chr12:51702400-51709600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:51702400-51712200	Weak transcription	GM12878-XiMat	blood

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