Variant report

Variant	rs12615518
Chromosome Location	chr2:99484808-99484809
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99223862..99225617-chr2:99483733..99486358,2	MCF-7	breast:
2	chr2:99454965..99457763-chr2:99481942..99484903,2	MCF-7	breast:
3	chr2:99484412..99487919-chr2:99523957..99528531,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238830	Chromatin interaction
ENSG00000196872	Chromatin interaction
ENSG00000115446	Chromatin interaction
ENSG00000183513	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12611969	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12612736	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12616060	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12616866	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12617554	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12619244	0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12620812	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12622254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622445	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12623022	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623171	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623172	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2871242	0.93[AMR][1000 genomes]
rs35979410	0.96[AMR][1000 genomes]
rs56943554	0.96[AMR][1000 genomes]
rs57480100	0.96[AMR][1000 genomes]
rs61419135	0.96[AMR][1000 genomes]
rs61552487	0.96[AMR][1000 genomes]
rs61604726	0.96[AMR][1000 genomes]
rs6760422	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72958631	0.93[AMR][1000 genomes]
rs7557719	0.89[AMR][1000 genomes]
rs868921	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99463400-99485400	Weak transcription	Gastric	stomach
2	chr2:99478600-99485400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:99480400-99485800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:99481400-99485000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:99481400-99485000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:99481400-99485200	Enhancers	HMEC	breast
7	chr2:99481400-99486400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:99481400-99486400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:99481800-99487000	Weak transcription	Lung	lung
10	chr2:99482000-99485200	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr2:99482200-99485400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr2:99482400-99485400	Enhancers	HUVEC	blood vessel
13	chr2:99482400-99485800	Enhancers	Muscle Satellite Cultured Cells	--
14	chr2:99482800-99485000	Weak transcription	Osteobl	bone
15	chr2:99483000-99485000	Weak transcription	HSMMtube	muscle
16	chr2:99483000-99486000	Weak transcription	HSMM	muscle
17	chr2:99483400-99485000	Weak transcription	NH-A	brain
18	chr2:99483800-99485000	Weak transcription	Fetal Muscle Leg	muscle
19	chr2:99483800-99485200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:99484000-99489000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:99484200-99485000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:99484200-99485000	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr2:99484200-99485200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr2:99484200-99486600	Flanking Active TSS	Hela-S3	cervix
25	chr2:99484400-99485200	Enhancers	Brain Angular Gyrus	brain
26	chr2:99484400-99485600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:99484600-99485000	Enhancers	Pancreas	Pancrea
28	chr2:99484600-99485000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr2:99484600-99485200	Flanking Active TSS	Stomach Mucosa	stomach
30	chr2:99484600-99485400	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr2:99484600-99485400	Flanking Active TSS	HepG2	liver
32	chr2:99484600-99485600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:99484600-99485800	Enhancers	Brain Anterior Caudate	brain
34	chr2:99484600-99486200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr2:99484600-99486400	Flanking Active TSS	NHEK	skin
36	chr2:99484800-99485000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:99484800-99485000	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr2:99484800-99486200	Active TSS	Esophagus	oesophagus
39	chr2:99484800-99486200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:99484800-99486400	Flanking Active TSS	Fetal Intestine Large	intestine

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