Variant report

Variant	rs11679686
Chromosome Location	chr2:11736037-11736038
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11733968..11736190-chr2:11742659..11745158,2	K562	blood:
2	chr2:11734732..11736294-chr2:11737996..11740139,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10165819	0.88[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10200851	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10929759	0.85[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11674605	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12468019	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12470971	0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12473442	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12993278	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13016186	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13017593	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13394619	0.91[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2358040	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2884374	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669752	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4669753	0.86[ASN][1000 genomes]
rs4669754	0.86[ASN][1000 genomes]
rs57439315	0.87[ASN][1000 genomes]
rs59129126	0.86[ASN][1000 genomes]
rs6746291	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7576826	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9287734	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9678410	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9789414	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9798272	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3359856	chr2:11735526-11738274	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv3392487	chr2:11735751-11738049	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11679686	GREB1	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11694800-11755200	Weak transcription	Gastric	stomach
3	chr2:11700000-11767000	Weak transcription	Right Atrium	heart
4	chr2:11711600-11738600	Weak transcription	Left Ventricle	heart
5	chr2:11714400-11765000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:11717600-11767000	Weak transcription	Fetal Intestine Small	intestine
7	chr2:11719200-11738000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:11719400-11750800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:11723000-11740400	Weak transcription	Liver	Liver
10	chr2:11723400-11740000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:11723600-11738600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:11724400-11738000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:11724400-11738600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:11724400-11788600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:11724600-11741000	Weak transcription	Brain Anterior Caudate	brain
16	chr2:11724600-11766800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:11724600-11766800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:11724800-11749600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:11725000-11743800	Weak transcription	Fetal Kidney	kidney
20	chr2:11725400-11742400	Strong transcription	Ovary	ovary
21	chr2:11725600-11766800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:11732800-11736800	Strong transcription	Fetal Stomach	stomach
23	chr2:11733000-11736400	Strong transcription	Fetal Muscle Leg	muscle
24	chr2:11733400-11750800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:11733600-11737000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:11733600-11737000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:11733600-11750600	Weak transcription	Pancreas	Pancrea
28	chr2:11733600-11784000	Strong transcription	HepG2	liver
29	chr2:11735000-11737800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr2:11735200-11736200	Strong transcription	Fetal Lung	lung
31	chr2:11735200-11736600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
32	chr2:11735200-11738400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr2:11735200-11744600	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr2:11735200-11746400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:11735400-11736200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:11735400-11736200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:11735400-11736200	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr2:11735400-11736400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:11735400-11736400	Strong transcription	Brain Substantia Nigra	brain
40	chr2:11735400-11736600	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr2:11735600-11736200	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:11735600-11736200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:11735600-11736400	Strong transcription	Brain Angular Gyrus	brain
44	chr2:11735600-11745000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:11735600-11746600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:11736000-11736400	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:11736000-11737400	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:11736000-11737800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:11736000-11743000	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links