Variant report

Variant	rs12468002
Chromosome Location	chr2:190240405-190240406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190238500..190240603-chr2:190242623..190245183,2	MCF-7	breast:
2	chr2:190235250..190237838-chr2:190239605..190241943,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12476438	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6414124	0.83[ASN][1000 genomes]
rs7560722	0.89[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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers 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	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv875614	chr2:190110841-190254758	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3451292	chr2:190225623-190266276	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv963941	chr2:190238972-190244573	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12468002	COL5A2	cis	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190233400-190241400	Enhancers	Muscle Satellite Cultured Cells	--
2	chr2:190235000-190243800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:190235400-190243800	Weak transcription	Aorta	Aorta
4	chr2:190235800-190241800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:190235800-190243600	Weak transcription	NHLF	lung
6	chr2:190236000-190241800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:190236000-190243600	Weak transcription	NH-A	brain
8	chr2:190236000-190243800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:190236000-190243800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:190236400-190243600	Weak transcription	HSMM	muscle
11	chr2:190237200-190240600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:190237600-190240800	Enhancers	Osteobl	bone
13	chr2:190238000-190241800	Weak transcription	NHEK	skin
14	chr2:190238800-190241400	Weak transcription	Fetal Intestine Large	intestine
15	chr2:190238800-190243600	Weak transcription	NHDF-Ad	bronchial
16	chr2:190238800-190243800	Weak transcription	HMEC	breast
17	chr2:190239400-190243800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:190239600-190240600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:190239600-190242400	Enhancers	A549	lung
20	chr2:190240200-190241000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:190240200-190241400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links