Variant report

Variant	rs17776879
Chromosome Location	chr5:58346667-58346668
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58336451..58338287-chr5:58345449..58347725,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10068543	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs10514870	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13183985	0.89[CHB][hapmap]
rs1498603	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62356693	1.00[AFR][1000 genomes]
rs6864156	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6889456	1.00[CHB][hapmap]
rs7706419	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7736186	1.00[AFR][1000 genomes]
rs986067	1.00[CHB][hapmap];0.88[JPT][hapmap]

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	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS 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
3	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
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58336200-58375600	Weak transcription	Left Ventricle	heart
2	chr5:58336600-58348000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58336600-58351800	Weak transcription	Fetal Intestine Small	intestine
4	chr5:58336600-58358000	Weak transcription	Fetal Intestine Large	intestine
5	chr5:58336600-58358000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:58337400-58359000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:58338200-58347600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:58338400-58350200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:58338800-58351800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:58338800-58359200	Weak transcription	Fetal Muscle Leg	muscle
11	chr5:58338800-58362000	Weak transcription	Gastric	stomach
12	chr5:58339000-58351600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:58339000-58365200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:58340600-58359000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr5:58343600-58356400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:58344400-58347600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:58345600-58347600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:58345600-58349200	Genic enhancers	A549	lung
19	chr5:58346000-58359000	Weak transcription	Stomach Mucosa	stomach
20	chr5:58346600-58348000	Strong transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links