Variant report

Variant	rs665200
Chromosome Location	chr3:135995016-135995017
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135967984..135969714-chr3:135993096..135996031,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114054	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1153871	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12330635	0.88[ASN][1000 genomes]
rs1278719	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1279425	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1279840	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1291921	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1618069	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1711171	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3755636	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4678428	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483465	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs523118	0.82[EUR][1000 genomes]
rs534944	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs548288	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs576771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs606725	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs632016	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs650505	0.99[ASN][1000 genomes]
rs667920	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6770476	0.80[ASN][1000 genomes]
rs684773	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs695983	0.85[ASN][1000 genomes]
rs696516	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72493178	0.88[ASN][1000 genomes]
rs73222262	0.87[ASN][1000 genomes]
rs7628146	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653249	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9832813	0.80[ASN][1000 genomes]
rs9848883	0.88[ASN][1000 genomes]
rs9856769	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970200-135996000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:135970400-135995400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:135970600-135998800	Weak transcription	Fetal Brain Male	brain
4	chr3:135970600-135999200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:135970600-135999200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:135970800-135995400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:135970800-135998000	Weak transcription	Hela-S3	cervix
9	chr3:135974800-135997800	Weak transcription	Stomach Mucosa	stomach
10	chr3:135976200-135996000	Weak transcription	Pancreas	Pancrea
11	chr3:135976200-135999400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:135976200-136012400	Weak transcription	NHLF	lung
13	chr3:135976200-136016400	Weak transcription	Colonic Mucosa	Colon
14	chr3:135976200-136021600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:135977400-135995600	Weak transcription	Fetal Lung	lung
16	chr3:135977400-135996000	Weak transcription	K562	blood
17	chr3:135977600-135995400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:135980800-135995600	Weak transcription	Right Ventricle	heart
19	chr3:135980800-135997600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:135980800-135999200	Weak transcription	Small Intestine	intestine
21	chr3:135981000-135995200	Weak transcription	Brain Germinal Matrix	brain
22	chr3:135981000-135995400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:135981000-135995400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:135981000-135998600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:135981200-135999200	Weak transcription	NHDF-Ad	bronchial
26	chr3:135981200-136052000	Weak transcription	NH-A	brain
27	chr3:135981600-135995200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:135981600-135997200	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:135981600-135998000	Weak transcription	Fetal Heart	heart
30	chr3:135981600-135998800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:135981600-136020400	Weak transcription	HUVEC	blood vessel
32	chr3:135981800-135995600	Weak transcription	Gastric	stomach
33	chr3:135981800-135999600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:135982400-135995200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:135982600-135997800	Weak transcription	HSMMtube	muscle
36	chr3:135982600-135999000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:135982600-136004000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:135982800-135995400	Weak transcription	Left Ventricle	heart
39	chr3:135982800-135995600	Weak transcription	Lung	lung
40	chr3:135982800-135995800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr3:135983000-135995200	Weak transcription	Brain Angular Gyrus	brain
42	chr3:135983200-135995200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:135983200-135995400	Weak transcription	Adipose Nuclei	Adipose
44	chr3:135983400-135995200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr3:135983600-135995200	Weak transcription	HepG2	liver
46	chr3:135983600-135995400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:135984000-135996400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:135984600-135995200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:135984600-135995800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:135984600-135996600	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links