Variant report

Variant	rs3136292
Chromosome Location	chr2:48020382-48020383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48010105..48013325-chr2:48019478..48022411,3	MCF-7	breast:
2	chr2:48016148..48017945-chr2:48020322..48022937,3	K562	blood:
3	chr2:48018260..48021014-chr2:48021762..48023287,2	K562	blood:
4	chr2:48018108..48020891-chr2:48025163..48028122,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116062	Chromatin interaction
ENSG00000235369	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1800935	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2159886	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2348243	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3136228	0.80[AMR][1000 genomes]
rs3136237	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3136250	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136262	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3136267	0.81[AMR][1000 genomes]
rs3136272	0.83[AMR][1000 genomes]
rs57632619	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58419715	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60444285	0.89[AMR][1000 genomes];0.88[EUR][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	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48011800-48023000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:48011800-48026200	Weak transcription	Stomach Mucosa	stomach
3	chr2:48012000-48022800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:48012000-48023000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:48012000-48023400	Weak transcription	HSMMtube	muscle
6	chr2:48012000-48024400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:48012000-48024600	Weak transcription	Aorta	Aorta
8	chr2:48012000-48024600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:48012000-48024800	Weak transcription	NHEK	skin
10	chr2:48012000-48026000	Weak transcription	Esophagus	oesophagus
11	chr2:48012000-48026000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:48012000-48026200	Weak transcription	Gastric	stomach
13	chr2:48012200-48021200	Weak transcription	HMEC	breast
14	chr2:48012200-48021600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:48012200-48021600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:48012200-48022000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:48012200-48022200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:48012200-48022200	Weak transcription	Osteobl	bone
19	chr2:48012200-48023000	Weak transcription	NHLF	lung
20	chr2:48012200-48023600	Weak transcription	Left Ventricle	heart
21	chr2:48012200-48024600	Weak transcription	Right Ventricle	heart
22	chr2:48012200-48026000	Weak transcription	Small Intestine	intestine
23	chr2:48012200-48030000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:48012600-48023000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:48012600-48023800	Weak transcription	Colonic Mucosa	Colon
26	chr2:48012600-48065000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:48013200-48021600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:48013400-48021200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:48013400-48021200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:48013400-48021400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:48013400-48021400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:48013400-48021600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:48013400-48022200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:48013400-48022400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr2:48013400-48022400	Weak transcription	NHDF-Ad	bronchial
36	chr2:48013400-48022800	Weak transcription	HUVEC	blood vessel
37	chr2:48013400-48023000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:48013400-48023400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:48013400-48023600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:48013400-48023800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:48013400-48023800	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:48013400-48023800	Weak transcription	Fetal Brain Male	brain
43	chr2:48013400-48024200	Weak transcription	Fetal Heart	heart
44	chr2:48013400-48025800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr2:48013600-48021800	Weak transcription	Brain Anterior Caudate	brain
46	chr2:48013600-48022200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:48014000-48023000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr2:48014200-48021600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:48014200-48022400	Weak transcription	Brain Angular Gyrus	brain
50	chr2:48014200-48023000	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links