Variant report

Variant	rs2286044
Chromosome Location	chr12:120571084-120571085
allele	A/C
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	chr12:120568196..120572672-chr12:120576593..120580624,4	K562	blood:
2	chr12:120568619..120571551-chr12:120574551..120576415,2	K562	blood:
3	chr12:120569732..120572593-chr12:120637429..120638936,2	MCF-7	breast:
4	chr12:120554472..120557367-chr12:120570703..120573027,2	K562	blood:
5	chr12:120568428..120573002-chr12:120580087..120584233,4	MCF-7	breast:
6	chr12:120554685..120559906-chr12:120569138..120571499,5	MCF-7	breast:
7	chr12:120569277..120571459-chr12:120572398..120574057,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000089154	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000089157	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10849739	0.85[JPT][hapmap]
rs11065028	0.96[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11065035	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11065036	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11065061	0.95[JPT][hapmap]
rs11833158	0.83[EUR][1000 genomes]
rs12164847	0.94[JPT][hapmap]
rs12305184	0.82[EUR][1000 genomes]
rs12306075	0.82[EUR][1000 genomes]
rs12310433	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12312562	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12578300	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2074540	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2238155	0.92[CEU][hapmap]
rs2238157	0.95[JPT][hapmap]
rs2239208	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2240314	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240315	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240317	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2240318	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2240319	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2240320	0.87[EUR][1000 genomes]
rs2240321	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2240322	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2240323	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2240325	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2269940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269941	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2269943	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2269944	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2269945	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2283362	1.00[CEU][hapmap]
rs2286043	0.99[EUR][1000 genomes]
rs2286045	0.88[EUR][1000 genomes]
rs2286049	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2286050	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2286051	0.80[EUR][1000 genomes]
rs3759397	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3815210	0.93[EUR][1000 genomes]
rs3888587	0.95[JPT][hapmap]
rs3956833	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4767886	0.95[JPT][hapmap]
rs59601514	0.84[EUR][1000 genomes]
rs60271600	0.83[EUR][1000 genomes]
rs7133235	0.82[EUR][1000 genomes]
rs7134706	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7135914	0.82[EUR][1000 genomes]
rs7299429	0.81[EUR][1000 genomes]
rs7301660	0.95[EUR][1000 genomes]
rs7966099	0.95[JPT][hapmap]
rs7978061	0.83[EUR][1000 genomes]
rs9630281	0.82[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2286044	GCN1L1	cis	multi-tissue	Pritchard
rs2286044	GCN1L1	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120556800-120571800	Weak transcription	Fetal Brain Male	brain
2	chr12:120556800-120578200	Weak transcription	Fetal Heart	heart
3	chr12:120563000-120580200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:120563000-120580200	Strong transcription	A549	lung
5	chr12:120563000-120588000	Strong transcription	HSMM	muscle
6	chr12:120563000-120596800	Strong transcription	Stomach Smooth Muscle	stomach
7	chr12:120563000-120605600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:120563000-120629800	Strong transcription	Fetal Stomach	stomach
9	chr12:120563000-120630200	Strong transcription	Fetal Muscle Leg	muscle
10	chr12:120563200-120602800	Strong transcription	Brain Germinal Matrix	brain
11	chr12:120563200-120630400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:120563400-120616200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:120563400-120629200	Strong transcription	Fetal Intestine Small	intestine
14	chr12:120563400-120630200	Strong transcription	Fetal Thymus	thymus
15	chr12:120563600-120574600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:120563600-120580400	Strong transcription	Pancreas	Pancrea
17	chr12:120563600-120583600	Strong transcription	Fetal Brain Female	brain
18	chr12:120563600-120596400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:120563600-120602400	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:120563600-120603600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:120563600-120603800	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:120563600-120605600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:120563600-120626000	Strong transcription	Brain Cingulate Gyrus	brain
24	chr12:120563600-120626200	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr12:120563600-120629000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:120563600-120630200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:120563600-120630200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:120563600-120630200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr12:120563600-120630200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:120563600-120630200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr12:120563800-120581000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:120563800-120582600	Strong transcription	Liver	Liver
33	chr12:120563800-120602600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr12:120563800-120602600	Strong transcription	Primary T cells from cord blood	blood
35	chr12:120563800-120602600	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr12:120563800-120602800	Strong transcription	Dnd41	blood
37	chr12:120563800-120603600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:120563800-120629800	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr12:120563800-120630000	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr12:120563800-120630200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr12:120564000-120580800	Strong transcription	HMEC	breast
42	chr12:120564000-120581200	Strong transcription	NHEK	skin
43	chr12:120564000-120583400	Strong transcription	Hela-S3	cervix
44	chr12:120564000-120603600	Strong transcription	Brain Angular Gyrus	brain
45	chr12:120564000-120603800	Strong transcription	Thymus	Thymus
46	chr12:120564200-120594200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr12:120564200-120624400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:120564200-120629600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr12:120564400-120579200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr12:120564400-120597000	Strong transcription	HepG2	liver

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