Variant report

Variant	rs3986366
Chromosome Location	chr4:54196323-54196324
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54188711..54191602-chr4:54194336..54196357,3	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10007422	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11133257	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11731676	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11933772	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11945292	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13103971	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13113985	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13130986	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13152012	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1383983	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1481817	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1481818	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1481821	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17705869	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1871826	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2054588	0.86[AMR][1000 genomes]
rs28765170	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4103016	0.87[EUR][1000 genomes]
rs4385132	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4435800	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4472196	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4864743	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4864748	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56056061	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62324288	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62324326	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6554089	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6810608	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6839876	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6846461	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71597825	0.80[AMR][1000 genomes]
rs7441849	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7657388	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7682970	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7698145	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7699124	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs900111	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs922748	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9761504	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9998307	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[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	nsv1008593	chr4:54120297-54207769	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 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	chr4:54169800-54216200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:54170600-54230600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:54172600-54215400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:54174200-54212600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:54180000-54212800	Weak transcription	Primary B cells from cord blood	blood
6	chr4:54187800-54212800	Weak transcription	Dnd41	blood
7	chr4:54188200-54213800	Weak transcription	Right Ventricle	heart
8	chr4:54188200-54218200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:54188200-54231200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:54188400-54205600	Weak transcription	Fetal Intestine Small	intestine
11	chr4:54188400-54212800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:54188600-54196800	Weak transcription	Small Intestine	intestine
13	chr4:54188600-54202800	Weak transcription	Primary T cells from cord blood	blood
14	chr4:54188600-54215400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr4:54189600-54212800	Weak transcription	Osteobl	bone
16	chr4:54189800-54206400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:54190000-54213800	Weak transcription	HUVEC	blood vessel
18	chr4:54192200-54212600	Weak transcription	NHDF-Ad	bronchial
19	chr4:54192200-54212800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:54193800-54201000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:54193800-54203000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:54193800-54203800	Weak transcription	GM12878-XiMat	blood
23	chr4:54193800-54206200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:54193800-54212600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:54193800-54213400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:54194200-54204800	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links