Variant report

Variant	rs2239206
Chromosome Location	chr12:120676090-120676091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120642171..120684465-chr12:120719749..120734210,267	K562	blood:
2	chr12:120631699..120641379-chr12:120675218..120683260,16	K562	blood:
3	chr12:120656223..120689871-chr12:120720394..120738112,311	MCF-7	breast:
4	chr12:120657004..120683911-chr12:120723753..120737731,232	K562	blood:
5	chr12:120675377..120678015-chr12:120698703..120700333,2	K562	blood:

Variant related genes	Relation type
ENSG00000089154	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000123009	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000089157	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11065040	0.80[EUR][1000 genomes]
rs2240312	0.85[CEU][hapmap]
rs3742039	0.91[ASW][hapmap];0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7960120	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised 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	484 gene(s)	inside rSNPs	diseases
5	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
6	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers 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	436 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2239206	GCN1L1	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120665200-120692000	Enhancers	Placenta	Placenta
2	chr12:120665400-120676800	Enhancers	Fetal Heart	heart
3	chr12:120665400-120682200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr12:120665600-120682200	Enhancers	Left Ventricle	heart
5	chr12:120666000-120677200	Enhancers	Lung	lung
6	chr12:120666200-120686000	Enhancers	Placenta Amnion	Placenta Amnion
7	chr12:120669200-120676200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:120669400-120677400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:120669400-120677800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr12:120669600-120676800	Enhancers	K562	blood
11	chr12:120669800-120677000	Enhancers	Duodenum Mucosa	Duodenum
12	chr12:120669800-120678000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr12:120669800-120679400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:120669800-120687600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr12:120671200-120677200	Enhancers	Esophagus	oesophagus
16	chr12:120671800-120677000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:120671800-120682800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:120672000-120676800	Enhancers	Small Intestine	intestine
19	chr12:120672000-120677000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:120672000-120677400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:120672200-120680400	Enhancers	Fetal Thymus	thymus
22	chr12:120672400-120676800	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr12:120672600-120677000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:120672800-120677000	Genic enhancers	Fetal Intestine Small	intestine
25	chr12:120673200-120676800	Enhancers	NH-A	brain
26	chr12:120673400-120676800	Enhancers	Right Atrium	heart
27	chr12:120673400-120679000	Enhancers	Spleen	Spleen
28	chr12:120673800-120676600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:120673800-120676800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:120673800-120676800	Enhancers	Rectal Smooth Muscle	rectum
31	chr12:120673800-120677000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:120673800-120679000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:120673800-120682800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:120674000-120676400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr12:120674000-120677000	Enhancers	Brain Anterior Caudate	brain
36	chr12:120674000-120678000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:120674000-120678800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:120674000-120679200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:120674000-120679800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:120674200-120676400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:120674200-120676400	Enhancers	Colon Smooth Muscle	Colon
42	chr12:120674200-120677800	Weak transcription	HepG2	liver
43	chr12:120674200-120678400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:120674200-120679200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:120674200-120679200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr12:120674200-120682800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr12:120674200-120687600	Weak transcription	Fetal Kidney	kidney
48	chr12:120674400-120683400	Genic enhancers	Primary T cells fromperipheralblood	blood
49	chr12:120674600-120676400	Enhancers	Primary hematopoietic stem cells	blood
50	chr12:120674600-120677000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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