Variant report

Variant	rs4540689
Chromosome Location	chr1:172059346-172059347
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:172059201..172061771-chr1:172370034..172372067,2	MCF-7	breast:
2	chr1:172059250..172060005-chr1:172398255..172399186,4	MCF-7	breast:
3	chr1:172057858..172060800-chr1:172327369..172328971,2	MCF-7	breast:
4	chr1:172058604..172060338-chr1:172368296..172369500,16	MCF-7	breast:
5	chr1:172057836..172060153-chr1:172397391..172399451,2	MCF-7	breast:
6	chr1:172059029..172059772-chr1:172368194..172369295,4	MCF-7	breast:
7	chr1:172057250..172060072-chr1:172060422..172061961,2	K562	blood:
8	chr1:172059095..172060013-chr1:172369694..172372109,8	MCF-7	breast:
9	chr1:172047980..172049973-chr1:172059181..172061869,2	K562	blood:
10	chr1:172059051..172060007-chr1:172370843..172371887,3	MCF-7	breast:
11	chr1:171971821..171972449-chr1:172059078..172060039,2	MCF-7	breast:

No data

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10489297	1.00[CHB][hapmap]
rs10910941	1.00[CHB][hapmap]
rs10914141	1.00[JPT][hapmap]
rs11584664	0.84[ASN][1000 genomes]
rs11584955	1.00[CHB][hapmap]
rs11589142	1.00[CHB][hapmap]
rs11589349	0.84[ASN][1000 genomes]
rs12123334	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12129264	1.00[CHB][hapmap]
rs12145177	1.00[JPT][hapmap]
rs16843855	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16843860	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17277008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17277127	1.00[CHB][hapmap]
rs17346438	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17346452	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17346473	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17350544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17350579	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17350586	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17361789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17361920	1.00[CHB][hapmap]
rs17472925	1.00[JPT][hapmap]
rs2209096	1.00[CHB][hapmap]
rs2421990	1.00[CHB][hapmap]
rs2421991	1.00[CHB][hapmap]
rs593688	1.00[CHB][hapmap]
rs61805853	0.92[ASN][1000 genomes]
rs61807762	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807763	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807784	0.84[ASN][1000 genomes]
rs61807786	0.84[ASN][1000 genomes]
rs61807787	0.84[ASN][1000 genomes]
rs628479	1.00[CHB][hapmap]
rs6694089	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 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	chr1:172040600-172076600	Weak transcription	Brain Angular Gyrus	brain
2	chr1:172041200-172060800	Weak transcription	Brain Substantia Nigra	brain
3	chr1:172041400-172061600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:172041600-172061800	Weak transcription	Brain Anterior Caudate	brain
5	chr1:172041800-172061200	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:172046600-172076800	Weak transcription	Fetal Brain Female	brain
7	chr1:172048000-172083800	Weak transcription	Aorta	Aorta
8	chr1:172049400-172110800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:172049600-172059400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:172052400-172060800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:172052400-172091600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:172057600-172059400	Weak transcription	Fetal Stomach	stomach
13	chr1:172057800-172060600	Weak transcription	Ovary	ovary
14	chr1:172057800-172074000	Weak transcription	Fetal Lung	lung
15	chr1:172058800-172060000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr1:172059000-172059400	Flanking Active TSS	Fetal Intestine Small	intestine
17	chr1:172059000-172059600	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr1:172059200-172059400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:172059200-172059600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr1:172059200-172059600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:172059200-172059600	Active TSS	Duodenum Mucosa	Duodenum
22	chr1:172059200-172059600	Active TSS	Fetal Intestine Large	intestine
23	chr1:172059200-172059600	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr1:172059200-172059600	Enhancers	Rectal Smooth Muscle	rectum
25	chr1:172059200-172059600	Enhancers	A549	lung
26	chr1:172059200-172059600	Flanking Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links