Variant report

Variant	rs3136283
Chromosome Location	chr2:48018479-48018480
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48013018..48016361-chr2:48016765..48019577,4	K562	blood:
2	chr2:48008394..48011813-chr2:48016879..48019860,3	K562	blood:
3	chr2:48016706..48019633-chr2:48029423..48031526,2	K562	blood:
4	chr2:48018260..48021014-chr2:48021762..48023287,2	K562	blood:
5	chr2:48018108..48020891-chr2:48025163..48028122,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251872	Chromatin interaction
ENSG00000235369	Chromatin interaction
ENSG00000116062	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1042820	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1800932	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3136235	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3136240	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136241	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3136247	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3136249	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3136269	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136279	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3136284	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3136288	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136315	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55927047	0.98[AMR][1000 genomes];0.92[EUR][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	nsv873999	chr2:47916074-48019485	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3136283	MSH6	cis	Thyroid	GTEx

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	chr2:48012000-48019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:48012000-48022800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:48012000-48023000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:48012000-48023400	Weak transcription	HSMMtube	muscle
7	chr2:48012000-48024400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:48012000-48024600	Weak transcription	Aorta	Aorta
9	chr2:48012000-48024600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:48012000-48024800	Weak transcription	NHEK	skin
11	chr2:48012000-48026000	Weak transcription	Esophagus	oesophagus
12	chr2:48012000-48026000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:48012000-48026200	Weak transcription	Gastric	stomach
14	chr2:48012200-48019800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:48012200-48021200	Weak transcription	HMEC	breast
16	chr2:48012200-48021600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:48012200-48021600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:48012200-48022000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:48012200-48022200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:48012200-48022200	Weak transcription	Osteobl	bone
21	chr2:48012200-48023000	Weak transcription	NHLF	lung
22	chr2:48012200-48023600	Weak transcription	Left Ventricle	heart
23	chr2:48012200-48024600	Weak transcription	Right Ventricle	heart
24	chr2:48012200-48026000	Weak transcription	Small Intestine	intestine
25	chr2:48012200-48030000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:48012400-48019400	Weak transcription	NH-A	brain
27	chr2:48012600-48023000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:48012600-48023800	Weak transcription	Colonic Mucosa	Colon
29	chr2:48012600-48065000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:48013200-48021600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:48013400-48018600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:48013400-48019400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:48013400-48019400	Weak transcription	Fetal Lung	lung
34	chr2:48013400-48019600	Weak transcription	Liver	Liver
35	chr2:48013400-48021200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr2:48013400-48021200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:48013400-48021400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:48013400-48021400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:48013400-48021600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:48013400-48022200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:48013400-48022400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr2:48013400-48022400	Weak transcription	NHDF-Ad	bronchial
43	chr2:48013400-48022800	Weak transcription	HUVEC	blood vessel
44	chr2:48013400-48023000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:48013400-48023400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:48013400-48023600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:48013400-48023800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:48013400-48023800	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:48013400-48023800	Weak transcription	Fetal Brain Male	brain
50	chr2:48013400-48024200	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links