Variant report

Variant	rs2409631
Chromosome Location	chr5:58527396-58527397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10059053	1.00[CHB][hapmap]
rs1031197	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10491352	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10940644	1.00[JPT][hapmap]
rs11954668	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11959132	1.00[JPT][hapmap]
rs11959567	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12519611	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1445948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1445953	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1445954	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1471429	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471430	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889479	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17444185	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17528522	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17628114	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17780175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1824157	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1838733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867711	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1947090	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2021775	1.00[JPT][hapmap]
rs2028836	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2081106	1.00[JPT][hapmap]
rs28862729	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700325	1.00[JPT][hapmap]
rs4700327	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4700328	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs67196739	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67526430	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6858946	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6877256	1.00[CHB][hapmap]
rs6877508	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6888028	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6891161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6897568	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765182	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7703022	1.00[CHB][hapmap]
rs7717303	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7719441	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1023570	chr5:58486384-58537849	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv881703	chr5:58517918-58540847	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1025807	chr5:58520050-58548231	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv520721	chr5:58520735-58558388	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58512800-58532400	Weak transcription	Pancreas	Pancrea
2	chr5:58516000-58530600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:58516200-58531000	Weak transcription	Psoas Muscle	Psoas
4	chr5:58519200-58535000	Weak transcription	Left Ventricle	heart
5	chr5:58519400-58529600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:58520800-58537000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:58521400-58532800	Weak transcription	Hela-S3	cervix
8	chr5:58526800-58527400	Enhancers	Colon Smooth Muscle	Colon
9	chr5:58526800-58528000	Genic enhancers	A549	lung
10	chr5:58527000-58528400	Enhancers	Fetal Heart	heart
11	chr5:58527200-58527400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:58527200-58527400	Enhancers	Aorta	Aorta
13	chr5:58527200-58528000	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links