Variant report

Variant	rs9852797
Chromosome Location	chr3:119640379-119640380
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119636239..119640440-chr3:119812716..119815351,4	MCF-7	breast:
2	chr3:119629935..119635391-chr3:119636173..119640969,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12330358	0.85[AFR][1000 genomes]
rs12330670	0.85[AFR][1000 genomes]
rs13315412	0.92[AFR][1000 genomes]
rs13316265	0.85[AFR][1000 genomes]
rs13319151	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs13319559	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs13319825	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs13323804	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs28481299	0.85[AFR][1000 genomes]
rs28540006	0.85[AFR][1000 genomes]
rs28709836	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs28817295	0.92[AFR][1000 genomes]
rs6769820	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6772172	0.87[YRI][hapmap];0.92[AFR][1000 genomes]
rs6778773	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs6796719	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7639665	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7639675	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9289137	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9289139	0.89[AFR][1000 genomes]
rs9810851	0.92[AFR][1000 genomes]
rs9816765	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9816864	0.92[AFR][1000 genomes]
rs9819836	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9825770	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9826355	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9831646	1.00[YRI][hapmap]
rs9835672	0.92[AFR][1000 genomes]
rs9836177	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9836325	0.92[AFR][1000 genomes]
rs9837710	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9840111	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9841959	0.92[AFR][1000 genomes]
rs9842216	0.92[AFR][1000 genomes]
rs9842542	0.92[AFR][1000 genomes]
rs9843873	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9852118	0.92[AFR][1000 genomes]
rs9854117	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9857139	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs9857548	0.92[AFR][1000 genomes]
rs9858471	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9861481	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9862099	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9864153	0.92[AFR][1000 genomes]
rs9869296	1.00[YRI][hapmap]
rs9871701	0.92[AFR][1000 genomes]
rs9871925	0.92[AFR][1000 genomes]
rs9872693	0.92[AFR][1000 genomes]
rs9874110	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9880833	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9881985	1.00[YRI][hapmap];0.92[AFR][1000 genomes]

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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119546000-119663400	Weak transcription	Lung	lung
2	chr3:119597600-119659000	Weak transcription	Gastric	stomach
3	chr3:119608000-119643600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:119608200-119677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:119611200-119643400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:119611200-119667000	Weak transcription	Pancreas	Pancrea
7	chr3:119611400-119642000	Weak transcription	Fetal Brain Male	brain
8	chr3:119611400-119649400	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:119611400-119682200	Weak transcription	HSMMtube	muscle
10	chr3:119614200-119645200	Weak transcription	K562	blood
11	chr3:119622200-119640800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:119624600-119642200	Weak transcription	Brain Germinal Matrix	brain
13	chr3:119625000-119668200	Weak transcription	Hela-S3	cervix
14	chr3:119627800-119640400	Weak transcription	Brain Substantia Nigra	brain
15	chr3:119628200-119643000	Weak transcription	Ovary	ovary
16	chr3:119628200-119643800	Weak transcription	Left Ventricle	heart
17	chr3:119628200-119655600	Weak transcription	Fetal Heart	heart
18	chr3:119628200-119663200	Weak transcription	Right Atrium	heart
19	chr3:119628400-119651000	Weak transcription	Right Ventricle	heart
20	chr3:119629600-119672200	Weak transcription	Fetal Stomach	stomach
21	chr3:119630200-119645400	Weak transcription	HUVEC	blood vessel
22	chr3:119630800-119663200	Weak transcription	Esophagus	oesophagus
23	chr3:119630800-119697400	Weak transcription	Thymus	Thymus
24	chr3:119631000-119642800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:119631000-119644000	Weak transcription	Psoas Muscle	Psoas
26	chr3:119631000-119717000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:119631200-119647800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:119631200-119650400	Weak transcription	Small Intestine	intestine
29	chr3:119631400-119642800	Weak transcription	Liver	Liver
30	chr3:119631400-119643000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:119631400-119643200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr3:119631400-119644000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:119631400-119646200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:119631400-119660800	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:119631600-119641600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:119631600-119656000	Weak transcription	NHEK	skin
37	chr3:119631800-119643000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:119632200-119645400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr3:119633000-119643000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:119633400-119655600	Weak transcription	Fetal Kidney	kidney
41	chr3:119634000-119656200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr3:119634600-119641000	Weak transcription	NHDF-Ad	bronchial
43	chr3:119634800-119641800	Weak transcription	NH-A	brain
44	chr3:119635000-119649400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:119635000-119652000	Weak transcription	Adipose Nuclei	Adipose
46	chr3:119635000-119665400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:119635000-119667000	Weak transcription	Placenta	Placenta
48	chr3:119635400-119664600	Weak transcription	HMEC	breast
49	chr3:119636200-119645400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:119636400-119667200	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links