Variant report

Variant	rs9295
Chromosome Location	chr2:36777825-36777826
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	chr2:36773310..36776281-chr2:36777076..36779151,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10172196	0.92[ASW][hapmap];0.86[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10181664	0.90[EUR][1000 genomes]
rs10189344	0.83[CEU][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1045543	0.83[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11681392	0.86[MEX][hapmap]
rs11691767	0.83[EUR][1000 genomes]
rs12105545	0.81[MEX][hapmap]
rs1533949	0.89[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.85[ASN][1000 genomes]
rs3755196	0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs711245	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010985	chr2:36707157-36942066	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer 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	12 gene(s)	inside rSNPs	diseases
2	nsv535642	chr2:36707157-36942066	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9295	CRIM1	cis	cerebellum	SCAN
rs9295	STRN	cis	cerebellum	SCAN
rs9295	FEZ2	cis	cerebellum	SCAN
rs9295	FEZ2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36713800-36789600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:36729600-36790200	Weak transcription	Small Intestine	intestine
3	chr2:36739000-36778200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:36750800-36783200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:36751000-36824200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:36753800-36782600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:36758000-36778400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:36758400-36779200	Weak transcription	Brain Angular Gyrus	brain
9	chr2:36760000-36782000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:36762400-36783200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:36762800-36783800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:36763000-36778600	Genic enhancers	HUVEC	blood vessel
13	chr2:36763200-36784200	Strong transcription	HepG2	liver
14	chr2:36763200-36785200	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr2:36763600-36779200	Strong transcription	Primary B cells from cord blood	blood
16	chr2:36763600-36779800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:36764000-36790200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:36764200-36783400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:36764200-36783800	Strong transcription	Fetal Intestine Large	intestine
20	chr2:36764400-36787200	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr2:36764800-36791800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:36765000-36778400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:36765600-36778800	Weak transcription	Gastric	stomach
24	chr2:36766000-36791800	Weak transcription	Esophagus	oesophagus
25	chr2:36766400-36788600	Weak transcription	Fetal Brain Male	brain
26	chr2:36766600-36781800	Weak transcription	K562	blood
27	chr2:36766800-36782800	Strong transcription	HMEC	breast
28	chr2:36766800-36783200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:36766800-36783400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:36767400-36780400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:36768200-36780600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:36768200-36781200	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:36769200-36782600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:36769800-36780400	Strong transcription	Adipose Nuclei	Adipose
35	chr2:36769800-36790400	Weak transcription	Spleen	Spleen
36	chr2:36770000-36778200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:36770000-36778400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:36770000-36780600	Strong transcription	Placenta	Placenta
39	chr2:36770000-36782000	Weak transcription	Colonic Mucosa	Colon
40	chr2:36770600-36780200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr2:36770800-36780200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:36771000-36778200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:36771000-36781400	Genic enhancers	A549	lung
44	chr2:36771000-36789000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:36771200-36780600	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:36771200-36788400	Weak transcription	Stomach Mucosa	stomach
47	chr2:36771400-36778600	Genic enhancers	Muscle Satellite Cultured Cells	--
48	chr2:36771400-36802800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:36771800-36782800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:36772400-36783800	Strong transcription	Duodenum Mucosa	Duodenum

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