Variant report

Variant	rs6741242
Chromosome Location	chr2:189675392-189675393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10191859	1.00[EUR][1000 genomes]
rs10201930	1.00[EUR][1000 genomes]
rs10497696	1.00[EUR][1000 genomes]
rs13306260	1.00[EUR][1000 genomes]
rs13425379	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16830983	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16830984	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17358566	1.00[CHD][hapmap]
rs28413125	1.00[EUR][1000 genomes]
rs41263781	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41272837	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61112771	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6711327	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6752549	1.00[EUR][1000 genomes]
rs73047634	1.00[EUR][1000 genomes]
rs7567045	1.00[EUR][1000 genomes]
rs7577467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7600151	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7607614	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs781283	1.00[CHD][hapmap]
rs8224	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003974	chr2:189331760-189827814	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1000932	chr2:189542210-189677277	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv536088	chr2:189542210-189677277	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv875606	chr2:189579045-189688463	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv875607	chr2:189579045-189711790	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1008847	chr2:189603961-189769705	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv997454	chr2:189615728-189770133	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1002175	chr2:189615728-189776301	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6741242	COL5A2	cis	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189668600-189675400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:189672800-189678400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:189673000-189675400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:189673000-189676800	Enhancers	NHDF-Ad	bronchial
5	chr2:189673000-189678400	Enhancers	Osteobl	bone
6	chr2:189673800-189677600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:189674200-189675600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:189674200-189676000	Weak transcription	NH-A	brain
9	chr2:189674400-189675400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:189674400-189676000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:189674400-189676000	Weak transcription	NHLF	lung
12	chr2:189674600-189677800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr2:189674600-189678600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:189675200-189676800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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