Variant report

Variant	rs256423
Chromosome Location	chr5:14351024-14351025
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14340281..14342656-chr5:14350736..14353309,2	MCF-7	breast:
2	chr5:14350928..14352625-chr5:14364251..14366443,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs154150	0.91[MEX][hapmap]
rs154152	0.87[EUR][1000 genomes]
rs154153	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs154154	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs154155	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs154159	0.97[ASN][1000 genomes]
rs154161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs165083	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1664507	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs247134	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs247139	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs247140	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247142	0.94[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs247143	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs247144	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs256416	0.82[ASN][1000 genomes]
rs256417	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs30623	0.82[JPT][hapmap]
rs30624	0.82[JPT][hapmap]
rs30769	0.87[EUR][1000 genomes]
rs30770	0.87[EUR][1000 genomes]
rs30771	0.86[EUR][1000 genomes]
rs30782	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30783	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs30784	0.89[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs30792	0.84[CEU][hapmap];0.87[CHB][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs39857	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs39866	0.94[ASN][1000 genomes]
rs409214	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs415341	0.86[EUR][1000 genomes]
rs42204	0.80[EUR][1000 genomes]
rs42259	0.84[CEU][hapmap];0.87[CHB][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs42405	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs42407	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs42551	0.94[CEU][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7700787	0.91[MEX][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	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3342821	chr5:14346652-14351350	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14335000-14360600	Weak transcription	Psoas Muscle	Psoas
2	chr5:14338000-14357200	Weak transcription	Colonic Mucosa	Colon
3	chr5:14338400-14358000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:14338800-14357600	Weak transcription	Esophagus	oesophagus
5	chr5:14339200-14357600	Weak transcription	Gastric	stomach
6	chr5:14339200-14358000	Weak transcription	Thymus	Thymus
7	chr5:14339200-14358200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:14339400-14358400	Weak transcription	Fetal Thymus	thymus
9	chr5:14340400-14353800	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr5:14340800-14353600	Strong transcription	HSMM	muscle
11	chr5:14341400-14355000	Weak transcription	Ovary	ovary
12	chr5:14341400-14359400	Weak transcription	Primary T cells from cord blood	blood
13	chr5:14341600-14357400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr5:14342600-14357200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr5:14342600-14358200	Weak transcription	Pancreas	Pancrea
16	chr5:14342800-14351600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:14342800-14352000	Strong transcription	Osteobl	bone
18	chr5:14342800-14352200	Strong transcription	NH-A	brain
19	chr5:14342800-14354000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr5:14342800-14355000	Weak transcription	Right Ventricle	heart
21	chr5:14342800-14357200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:14342800-14357200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:14342800-14365200	Weak transcription	Small Intestine	intestine
24	chr5:14343000-14351200	Strong transcription	Fetal Intestine Large	intestine
25	chr5:14343200-14351600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:14343200-14358800	Weak transcription	Brain Hippocampus Middle	brain
27	chr5:14343400-14352400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:14343400-14357000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr5:14343600-14351200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:14343600-14351200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr5:14343600-14357000	Weak transcription	Brain Angular Gyrus	brain
32	chr5:14343600-14357600	Weak transcription	Brain Anterior Caudate	brain
33	chr5:14343800-14362400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:14344400-14358000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr5:14345000-14355000	Weak transcription	Left Ventricle	heart
36	chr5:14345400-14353800	Weak transcription	Hela-S3	cervix
37	chr5:14345600-14351400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr5:14346000-14351800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr5:14346200-14352000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:14346200-14352200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:14346200-14352400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr5:14347000-14356400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:14347000-14358800	Weak transcription	Fetal Lung	lung
44	chr5:14347200-14352600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr5:14347200-14353800	Weak transcription	HUVEC	blood vessel
46	chr5:14347200-14355000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:14347200-14356600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr5:14347200-14357400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr5:14348400-14352000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:14348400-14354800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links