Variant report

Variant	rs6898082
Chromosome Location	chr5:58406404-58406405
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10065303	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs10452450	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs1115728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1115729	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs11957770	0.88[YRI][hapmap]
rs12109774	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs16889167	0.83[CEU][hapmap]
rs17720871	1.00[JPT][hapmap]
rs17721133	0.81[CEU][hapmap]
rs17721311	1.00[JPT][hapmap]
rs17721564	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs17721878	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17777280	1.00[JPT][hapmap]
rs17777617	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs62356686	0.82[EUR][1000 genomes]
rs62356687	0.82[EUR][1000 genomes]
rs62356690	0.82[EUR][1000 genomes]
rs62356691	0.82[EUR][1000 genomes]
rs62356692	0.83[EUR][1000 genomes]
rs62356694	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6880249	1.00[ASN][1000 genomes]
rs6898408	0.96[ASN][1000 genomes]
rs950446	0.92[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58396200-58420000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:58399400-58419400	Weak transcription	Fetal Intestine Small	intestine
3	chr5:58400800-58412200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:58401000-58407800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:58401000-58408000	Weak transcription	Fetal Brain Female	brain
6	chr5:58401000-58412200	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:58401000-58412400	Weak transcription	Right Atrium	heart
8	chr5:58401000-58413200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:58401000-58418600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:58401400-58411400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:58401800-58410600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:58403600-58412000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:58404000-58408000	Weak transcription	Pancreas	Pancrea
14	chr5:58404000-58408600	Genic enhancers	A549	lung
15	chr5:58404000-58411000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:58404000-58412400	Weak transcription	Psoas Muscle	Psoas
17	chr5:58404200-58412200	Weak transcription	Hela-S3	cervix
18	chr5:58404200-58414200	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:58405000-58407200	Enhancers	Adipose Nuclei	Adipose
20	chr5:58405400-58406600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr5:58405400-58411200	Weak transcription	HMEC	breast
22	chr5:58405800-58406600	Weak transcription	Left Ventricle	heart
23	chr5:58405800-58410400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr5:58406000-58407600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:58406000-58410600	Weak transcription	Fetal Heart	heart
26	chr5:58406200-58412400	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links