Variant report

Variant	rs57797139
Chromosome Location	chr3:113191088-113191089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:113190368..113192006-chr3:113232848..113234946,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163611	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs2270784	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2306792	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57006145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57251392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57357573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57414437	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57417572	0.87[ASN][1000 genomes]
rs57591967	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58121831	0.87[ASN][1000 genomes]
rs58248101	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58551767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58890779	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58992191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59275119	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59911537	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60633405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60874642	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61151383	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61258912	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6768642	0.87[ASN][1000 genomes]
rs6780086	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6790910	0.87[ASN][1000 genomes]
rs7619717	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7621031	0.87[ASN][1000 genomes]
rs7621039	0.87[ASN][1000 genomes]
rs7622062	0.87[ASN][1000 genomes]
rs775218	0.87[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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113160400-113191200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:113160400-113192800	Weak transcription	Stomach Mucosa	stomach
3	chr3:113160600-113203800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:113160800-113203800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:113160800-113203800	Weak transcription	Aorta	Aorta
6	chr3:113160800-113224800	Weak transcription	Placenta	Placenta
7	chr3:113160800-113232600	Weak transcription	Right Ventricle	heart
8	chr3:113161400-113192200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:113166600-113203800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:113169800-113191600	Weak transcription	Fetal Brain Male	brain
11	chr3:113172600-113203800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:113172800-113232800	Weak transcription	HSMMtube	muscle
13	chr3:113176400-113233200	Weak transcription	Gastric	stomach
14	chr3:113177400-113225800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:113177600-113224400	Weak transcription	Spleen	Spleen
16	chr3:113179600-113191200	Weak transcription	Brain Angular Gyrus	brain
17	chr3:113179600-113192200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:113179600-113192600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:113179600-113204000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:113179600-113215200	Weak transcription	HMEC	breast
21	chr3:113179600-113217200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:113179600-113232400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:113179600-113232800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:113182000-113191400	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:113182000-113203800	Weak transcription	Esophagus	oesophagus
26	chr3:113182000-113203800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:113184000-113233200	Weak transcription	Pancreas	Pancrea
28	chr3:113184800-113204800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:113187200-113203800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:113187200-113203800	Weak transcription	Ovary	ovary
31	chr3:113187200-113207200	Weak transcription	Thymus	Thymus
32	chr3:113187200-113224400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:113187400-113203800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:113187400-113203800	Weak transcription	Hela-S3	cervix
35	chr3:113187800-113191400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:113187800-113191400	Weak transcription	Fetal Intestine Small	intestine
37	chr3:113187800-113193400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr3:113187800-113193600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:113187800-113193600	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:113187800-113203800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:113187800-113203800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr3:113187800-113203800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:113187800-113204600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:113187800-113207000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:113187800-113209400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:113188000-113191200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:113188000-113203800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:113188000-113203800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:113188000-113203800	Weak transcription	Dnd41	blood
50	chr3:113188000-113206000	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links