Variant report

Variant	rs6888028
Chromosome Location	chr5:58545732-58545733
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11954668	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1445948	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1445952	0.81[ASN][1000 genomes]
rs1445954	0.86[ASN][1000 genomes]
rs1471429	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1471430	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16889479	0.86[ASN][1000 genomes]
rs16889499	0.86[ASN][1000 genomes]
rs16889518	0.81[ASN][1000 genomes]
rs17528522	0.81[ASN][1000 genomes]
rs17528578	0.81[ASN][1000 genomes]
rs1823070	0.86[ASN][1000 genomes]
rs1824157	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1838733	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1867711	0.86[ASN][1000 genomes]
rs1867712	0.86[ASN][1000 genomes]
rs1947090	0.81[ASN][1000 genomes]
rs2409631	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28862729	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4700327	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4700328	0.81[ASN][1000 genomes]
rs67196739	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67526430	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6858946	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877508	0.81[ASN][1000 genomes]
rs6897568	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs765182	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7717303	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58527400-58549800	Weak transcription	Aorta	Aorta
2	chr5:58535600-58551800	Weak transcription	HUVEC	blood vessel
3	chr5:58537600-58548600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:58537600-58553000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:58541200-58558400	Weak transcription	Pancreas	Pancrea
6	chr5:58541600-58560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:58541600-58562400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:58541800-58562800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:58542200-58551600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr5:58542600-58548600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:58543200-58545800	Genic enhancers	A549	lung
12	chr5:58543200-58552400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr5:58543600-58552200	Weak transcription	Fetal Intestine Large	intestine
14	chr5:58544400-58545800	Weak transcription	Psoas Muscle	Psoas
15	chr5:58544400-58547800	Weak transcription	Fetal Heart	heart
16	chr5:58544400-58551400	Weak transcription	Fetal Kidney	kidney
17	chr5:58544400-58553000	Weak transcription	Left Ventricle	heart
18	chr5:58545200-58548000	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:58545400-58548000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:58545400-58548400	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links