Variant report

Variant	rs12612593
Chromosome Location	chr2:173893332-173893333
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	chr2:173892252..173896882-chr2:173939144..173942444,6	MCF-7	breast:
2	chr2:173892758..173895374-chr2:173911350..173913199,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091428	Chromatin interaction
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12614386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12615974	1.00[ASN][1000 genomes]
rs12618296	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12621472	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12621641	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13034647	1.00[AFR][1000 genomes]
rs16861180	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16861185	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16861187	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16861206	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2290376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34252442	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35730673	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3754754	1.00[CEU][hapmap]
rs3769218	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769221	0.90[ASN][1000 genomes]
rs3769223	0.90[ASN][1000 genomes]
rs41268707	1.00[AFR][1000 genomes]
rs4296399	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6735942	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7585995	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173868000-173902000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:173877200-173901600	Weak transcription	Gastric	stomach
3	chr2:173881200-173912800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:173881400-173897200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:173887400-173894800	Weak transcription	Left Ventricle	heart
6	chr2:173888800-173905600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:173888800-173906600	Weak transcription	Lung	lung
8	chr2:173890600-173894000	Enhancers	NHDF-Ad	bronchial
9	chr2:173891000-173896200	Weak transcription	Placenta	Placenta
10	chr2:173891000-173908000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:173891400-173894000	Enhancers	Fetal Lung	lung
12	chr2:173891400-173894200	Enhancers	Colon Smooth Muscle	Colon
13	chr2:173891400-173896400	Enhancers	Fetal Heart	heart
14	chr2:173891600-173893600	Weak transcription	Liver	Liver
15	chr2:173892000-173894000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:173892000-173894000	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr2:173892000-173894000	Enhancers	Fetal Stomach	stomach
18	chr2:173892000-173894000	Enhancers	NHLF	lung
19	chr2:173892200-173893800	Enhancers	Stomach Mucosa	stomach
20	chr2:173892200-173894000	Enhancers	Rectal Smooth Muscle	rectum
21	chr2:173892200-173894600	Enhancers	Fetal Intestine Large	intestine
22	chr2:173892400-173893600	Enhancers	HSMMtube	muscle
23	chr2:173892400-173894000	Enhancers	Fetal Brain Male	brain
24	chr2:173892400-173894400	Enhancers	Fetal Intestine Small	intestine
25	chr2:173892600-173893400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:173892600-173893400	Enhancers	Duodenum Mucosa	Duodenum
27	chr2:173892600-173893600	Enhancers	Small Intestine	intestine
28	chr2:173892600-173893800	Enhancers	Fetal Brain Female	brain
29	chr2:173892600-173894000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:173892600-173894000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:173892600-173894000	Enhancers	Ovary	ovary
32	chr2:173892600-173894000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr2:173892600-173894200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr2:173892600-173897200	Enhancers	Fetal Muscle Leg	muscle
35	chr2:173892600-173897400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr2:173892600-173906800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:173892800-173894400	Weak transcription	Fetal Kidney	kidney
38	chr2:173892800-173894600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:173892800-173894800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:173892800-173895400	Weak transcription	NHEK	skin
41	chr2:173892800-173901600	Weak transcription	Pancreas	Pancrea
42	chr2:173892800-173902400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:173893000-173893800	Enhancers	Right Ventricle	heart
44	chr2:173893000-173895000	Weak transcription	HMEC	breast
45	chr2:173893000-173898600	Weak transcription	A549	lung
46	chr2:173893000-173900600	Weak transcription	Brain Angular Gyrus	brain
47	chr2:173893000-173908800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:173893000-173913200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:173893200-173893800	Weak transcription	Psoas Muscle	Psoas
50	chr2:173893200-173894000	Enhancers	Stomach Smooth Muscle	stomach

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