Variant report

Variant	rs17271071
Chromosome Location	chr2:190349911-190349912
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190347309..190351333-chr2:190419513..190421740,3	MCF-7	breast:
2	chr2:190349773..190352043-chr2:190405227..190407420,2	MCF-7	breast:
3	chr2:190348544..190350498-chr2:190356063..190358536,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10497701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10497702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1123109	1.00[ASW][hapmap]
rs11568351	1.00[ASW][hapmap]
rs11686908	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11688806	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1371470	0.90[ASN][1000 genomes]
rs1402369	0.82[ASN][1000 genomes]
rs17198857	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17198892	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17271036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17271043	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[ASN][1000 genomes]
rs17271057	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[ASN][1000 genomes]
rs17271183	1.00[ASW][hapmap]
rs2289225	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[ASN][1000 genomes]
rs2304701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs55822942	0.92[ASN][1000 genomes]
rs58584769	0.82[ASN][1000 genomes]
rs61410845	0.82[ASN][1000 genomes]
rs62182070	0.82[ASN][1000 genomes]
rs62184647	0.82[ASN][1000 genomes]
rs62184648	0.82[ASN][1000 genomes]
rs62184649	0.86[ASN][1000 genomes]
rs62184652	0.90[ASN][1000 genomes]
rs62184653	0.90[ASN][1000 genomes]
rs62187072	0.92[ASN][1000 genomes]
rs62187074	0.88[ASN][1000 genomes]
rs62187075	0.88[ASN][1000 genomes]
rs62187078	0.82[ASN][1000 genomes]
rs62187082	0.92[ASN][1000 genomes]
rs62187106	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6721290	0.86[ASN][1000 genomes]
rs6747132	0.86[ASN][1000 genomes]
rs72914175	0.86[ASN][1000 genomes]
rs7423067	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	nsv584062	chr2:190272195-190376493	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17271071	COL5A2	cis	cerebellum	SCAN
rs17271071	COL5A2	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190335000-190351800	Weak transcription	Psoas Muscle	Psoas
2	chr2:190335000-190366200	Weak transcription	Ovary	ovary
3	chr2:190335800-190352600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:190339600-190350000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:190339600-190352600	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:190340800-190352400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:190341600-190350800	Weak transcription	Liver	Liver
8	chr2:190341800-190351000	Weak transcription	HMEC	breast
9	chr2:190341800-190351200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:190342400-190357000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:190342800-190350000	Weak transcription	HSMM	muscle
12	chr2:190348000-190350000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr2:190348200-190350000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:190349200-190350400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:190349200-190365000	Weak transcription	Fetal Intestine Large	intestine
16	chr2:190349600-190350000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr2:190349600-190351400	Enhancers	HSMMtube	muscle
18	chr2:190349600-190351600	Weak transcription	Placenta	Placenta
19	chr2:190349800-190350200	Enhancers	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links