Variant report

Variant	rs2252958
Chromosome Location	chr2:11755443-11755444
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11753643..11756642-chr2:11757433..11758936,2	MCF-7	breast:
2	chr2:11754721..11756472-chr2:11760388..11762791,2	MCF-7	breast:
3	chr2:11753829..11755570-chr2:11758835..11761117,2	K562	blood:
4	chr2:11755207..11756875-chr2:11801472..11803866,2	K562	blood:
5	chr2:11621457..11624787-chr2:11753040..11757547,4	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11681838	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11688915	1.00[CHB][hapmap]
rs11689869	0.91[EUR][1000 genomes]
rs13421972	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs13431704	1.00[CHD][hapmap]
rs13432243	1.00[CHD][hapmap]
rs1435547	1.00[CHD][hapmap]
rs16857679	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1865575	1.00[CHD][hapmap]
rs2304399	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs34592059	0.88[EUR][1000 genomes]
rs3828298	0.89[CEU][hapmap]
rs4669756	1.00[CHB][hapmap]
rs55890755	0.97[EUR][1000 genomes]
rs6730352	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6735957	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6744817	1.00[CHD][hapmap]
rs71446421	0.97[EUR][1000 genomes]
rs7596162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2252958	GRHL1	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11700000-11767000	Weak transcription	Right Atrium	heart
3	chr2:11714400-11765000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:11717600-11767000	Weak transcription	Fetal Intestine Small	intestine
5	chr2:11724400-11788600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:11724600-11766800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:11724600-11766800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:11725600-11766800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:11733600-11784000	Strong transcription	HepG2	liver
10	chr2:11736200-11765000	Weak transcription	Fetal Lung	lung
11	chr2:11736800-11762800	Weak transcription	Fetal Heart	heart
12	chr2:11743200-11765200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:11743400-11765000	Weak transcription	Left Ventricle	heart
14	chr2:11745200-11765000	Weak transcription	Fetal Kidney	kidney
15	chr2:11747200-11767200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:11748000-11766800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:11748600-11767600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:11749000-11763200	Strong transcription	Fetal Stomach	stomach
19	chr2:11749000-11766800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:11749400-11763400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr2:11749600-11759600	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr2:11750000-11760200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:11750600-11757400	Strong transcription	Pancreas	Pancrea
24	chr2:11751600-11757000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:11752000-11784400	Strong transcription	Ovary	ovary
26	chr2:11752200-11761400	Weak transcription	Adipose Nuclei	Adipose
27	chr2:11752600-11757200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:11752800-11767200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:11753200-11758800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:11753400-11756600	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:11753400-11757000	Strong transcription	Brain Angular Gyrus	brain
32	chr2:11753400-11759400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:11754000-11757200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:11754200-11756400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:11754200-11759200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:11754200-11759600	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr2:11754200-11766600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr2:11754800-11759600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:11754800-11759800	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:11755000-11757200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:11755000-11758800	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:11755000-11759600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:11755200-11755600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:11755200-11756400	Strong transcription	Gastric	stomach
45	chr2:11755200-11757800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:11755200-11757800	Strong transcription	Pancreatic Islets	Pancreatic Islet
47	chr2:11755200-11759400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:11755200-11759600	Strong transcription	Brain Anterior Caudate	brain
49	chr2:11755200-11759600	Strong transcription	Brain Cingulate Gyrus	brain
50	chr2:11755200-11763000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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