Variant report

Variant	rs12297620
Chromosome Location	chr12:10772728-10772729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:10771079..10773905-chr12:10786792..10788770,2	K562	blood:
2	chr12:10765155..10768386-chr12:10770513..10774457,4	MCF-7	breast:
3	chr12:10770924..10772839-chr12:10825568..10827149,2	MCF-7	breast:
4	chr12:10771877..10773786-chr12:10773916..10777458,3	K562	blood:
5	chr12:10770221..10774557-chr12:10774772..10778392,5	K562	blood:

Variant related genes	Relation type
ENSG00000111196	Chromatin interaction
ENSG00000060140	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11053888	1.00[ASW][hapmap];0.87[LWK][hapmap];0.84[AFR][1000 genomes]
rs11053890	0.80[YRI][hapmap];0.82[AFR][1000 genomes]
rs11836109	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11836264	0.83[AMR][1000 genomes]
rs12299672	0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs12302213	0.90[AFR][1000 genomes]
rs12304304	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12304656	1.00[ASW][hapmap];0.81[LWK][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12311784	0.82[AFR][1000 genomes]
rs12315090	0.82[AFR][1000 genomes]
rs12319401	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs12322680	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2198964	0.81[AFR][1000 genomes]
rs55785135	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs57035205	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58677311	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59613394	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs60461379	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61473048	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7303851	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs74060455	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs74060473	0.82[AFR][1000 genomes]
rs7968001	0.82[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10766600-10787000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:10766600-10789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:10766600-10794400	Weak transcription	Gastric	stomach
4	chr12:10766800-10789400	Weak transcription	Esophagus	oesophagus
5	chr12:10767000-10778400	Weak transcription	Colonic Mucosa	Colon
6	chr12:10767200-10775000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:10767200-10780600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:10767200-10781200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:10767600-10776800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:10770200-10773000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:10770200-10774600	Enhancers	HSMMtube	muscle
12	chr12:10770600-10773000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:10770600-10777600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:10771200-10776000	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr12:10771400-10782200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:10771600-10772800	Weak transcription	K562	blood
17	chr12:10771600-10773200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:10771600-10775800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:10771800-10775400	Strong transcription	HUVEC	blood vessel
20	chr12:10771800-10775600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:10772000-10775200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr12:10772000-10775400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:10772000-10787200	Weak transcription	NHEK	skin
24	chr12:10772200-10773400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:10772200-10774600	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr12:10772400-10773000	Strong transcription	Primary hematopoietic stem cells	blood
27	chr12:10772400-10773000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:10772400-10773000	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:10772400-10773200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:10772400-10774000	Genic enhancers	HSMM	muscle
31	chr12:10772400-10774600	Weak transcription	NHDF-Ad	bronchial
32	chr12:10772400-10775800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:10772400-10780600	Weak transcription	HMEC	breast

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