Variant report

Variant	rs3936255
Chromosome Location	chr12:120546927-120546928
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120546217..120547890-chr12:120637360..120639116,2	MCF-7	breast:
2	chr12:120541333..120544024-chr12:120545087..120548824,4	K562	blood:
3	chr12:120516503..120519028-chr12:120545885..120547617,3	MCF-7	breast:
4	chr12:120537177..120551260-chr12:120551865..120557471,32	MCF-7	breast:
5	chr12:120530653..120533047-chr12:120546593..120548453,2	MCF-7	breast:
6	chr12:120539799..120542911-chr12:120545962..120548810,4	MCF-7	breast:
7	chr12:120544989..120547921-chr12:120551976..120557751,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000089157	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000135127	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10732609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774539	0.85[EUR][1000 genomes]
rs10774540	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3852585	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3852587	1.00[CEU][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs5028648	0.86[EUR][1000 genomes]
rs7961547	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3936255	OASL	cis	parietal	SCAN
rs3936255	GCN1L1	cis	parietal	SCAN
rs3936255	GCN1L1	cis	multi-tissue	Pritchard
rs3936255	SRSF9	cis	parietal	SCAN
rs3936255	WSB2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120525600-120551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:120525800-120553400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:120533800-120553000	Weak transcription	Fetal Kidney	kidney
4	chr12:120534400-120553200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:120534600-120547200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:120534600-120548200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:120539200-120552600	Weak transcription	Fetal Brain Male	brain
8	chr12:120539600-120551600	Weak transcription	Fetal Lung	lung
9	chr12:120539600-120552200	Strong transcription	Fetal Stomach	stomach
10	chr12:120540000-120547600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:120540000-120553000	Weak transcription	HSMMtube	muscle
12	chr12:120540800-120547200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:120541400-120547000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:120541600-120548400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:120541600-120551000	Weak transcription	HSMM	muscle
16	chr12:120541800-120548800	Weak transcription	K562	blood
17	chr12:120541800-120552600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:120541800-120552800	Weak transcription	Brain Substantia Nigra	brain
19	chr12:120541800-120552800	Weak transcription	NH-A	brain
20	chr12:120542200-120553000	Weak transcription	Aorta	Aorta
21	chr12:120542400-120547600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr12:120542400-120548200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:120542400-120552400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:120543000-120547800	Weak transcription	Brain Anterior Caudate	brain
25	chr12:120543000-120552800	Weak transcription	Osteobl	bone
26	chr12:120543200-120547800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:120543200-120547800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:120543200-120548200	Weak transcription	Small Intestine	intestine
29	chr12:120543400-120547800	Weak transcription	Stomach Mucosa	stomach
30	chr12:120543400-120549000	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:120543400-120551600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:120543400-120552600	Weak transcription	Ovary	ovary
33	chr12:120543400-120553000	Weak transcription	Fetal Heart	heart
34	chr12:120543400-120553600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:120544000-120547000	Strong transcription	Fetal Intestine Large	intestine
36	chr12:120544000-120548400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:120544000-120548600	Weak transcription	HUVEC	blood vessel
38	chr12:120544000-120552800	Weak transcription	Colonic Mucosa	Colon
39	chr12:120544200-120547600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:120544200-120547800	Weak transcription	Liver	Liver
41	chr12:120544200-120552200	Weak transcription	Hela-S3	cervix
42	chr12:120544400-120547600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:120544400-120547600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:120544400-120548200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:120544400-120548200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr12:120544400-120548400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr12:120544400-120552800	Weak transcription	NHDF-Ad	bronchial
48	chr12:120544400-120553200	Strong transcription	Fetal Intestine Small	intestine
49	chr12:120544800-120548200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:120545400-120547400	Strong transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links