Variant report

Variant	rs12658408
Chromosome Location	chr5:17021150-17021151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11133870	0.85[ASN][1000 genomes]
rs11133871	0.84[ASN][1000 genomes]
rs11744619	0.84[ASN][1000 genomes]
rs12517620	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34715075	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34891284	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34945488	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35081025	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4374758	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4409083	1.00[ASN][1000 genomes]
rs4446458	1.00[ASN][1000 genomes]
rs4513695	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56030047	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60930947	0.85[ASN][1000 genomes]
rs67553836	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6859425	0.94[ASN][1000 genomes]
rs6894767	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72734347	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7706916	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv3510797	chr5:16966764-17125849	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3510798	chr5:16966764-17125849	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1795984	chr5:16973769-17078295	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv1796588	chr5:17000364-17033610	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1017222	chr5:17001819-17133274	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1021972	chr5:17011758-17091878	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17013400-17021200	Weak transcription	A549	lung
2	chr5:17017800-17025600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:17018200-17022400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:17019400-17024800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:17019800-17024800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:17019800-17024800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:17019800-17024800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:17020000-17024800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:17020600-17021200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:17020600-17021200	Enhancers	NHEK	skin
11	chr5:17020800-17021200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:17020800-17021200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:17020800-17021200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:17020800-17021200	Active TSS	Adipose Nuclei	Adipose
15	chr5:17020800-17021200	Flanking Active TSS	Fetal Lung	lung
16	chr5:17020800-17021200	Active TSS	Rectal Mucosa Donor 31	rectum
17	chr5:17020800-17021400	Enhancers	Duodenum Mucosa	Duodenum
18	chr5:17020800-17021400	Active TSS	Stomach Smooth Muscle	stomach
19	chr5:17020800-17021400	Flanking Active TSS	HUVEC	blood vessel
20	chr5:17020800-17021400	Flanking Active TSS	NHLF	lung
21	chr5:17020800-17021800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr5:17020800-17022200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:17020800-17022600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:17021000-17021200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:17021000-17021200	Flanking Active TSS	Ovary	ovary
26	chr5:17021000-17021200	Active TSS	NHDF-Ad	bronchial
27	chr5:17021000-17021200	Active TSS	Osteobl	bone
28	chr5:17021000-17021400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:17021000-17021400	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr5:17021000-17021600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr5:17021000-17022000	Enhancers	Brain Hippocampus Middle	brain
32	chr5:17021000-17022600	Enhancers	HMEC	breast
33	chr5:17021000-17022600	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links