Variant report

Variant	rs2237470
Chromosome Location	chr7:50736158-50736159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2190495	0.82[CHB][hapmap]
rs2237442	0.81[CHB][hapmap]
rs2237471	0.95[CHB][hapmap]
rs2237474	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240500	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2244347	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2244351	0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs2244353	0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs2244372	0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs2244479	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2244480	0.83[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs2529410	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs2529411	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2529415	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2715135	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1032882	chr7:50611138-50775257	Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538834	chr7:50611138-50775257	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1031138	chr7:50651793-50814881	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2237470	ABCA13	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50706400-50744000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:50707200-50748600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:50710000-50743600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:50710000-50758200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:50715600-50740600	Weak transcription	Brain Germinal Matrix	brain
6	chr7:50716600-50740200	Weak transcription	Fetal Intestine Large	intestine
7	chr7:50720600-50739400	Enhancers	Right Atrium	heart
8	chr7:50722000-50737600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:50724200-50742800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:50725400-50737600	Enhancers	Psoas Muscle	Psoas
11	chr7:50726000-50741000	Weak transcription	Fetal Brain Female	brain
12	chr7:50727800-50737400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr7:50728400-50737600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:50729200-50737600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:50729800-50741600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr7:50730000-50736600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr7:50730000-50737200	Enhancers	Left Ventricle	heart
18	chr7:50730200-50744000	Weak transcription	Small Intestine	intestine
19	chr7:50730200-50748600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr7:50730400-50738600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:50731000-50741400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr7:50731400-50737600	Weak transcription	Thymus	Thymus
23	chr7:50731400-50743200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr7:50731800-50736600	Enhancers	NHDF-Ad	bronchial
25	chr7:50731800-50750000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:50732000-50737200	Enhancers	Liver	Liver
27	chr7:50732600-50749200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr7:50733200-50736200	Enhancers	Aorta	Aorta
29	chr7:50733200-50743600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr7:50733400-50736600	Enhancers	Ovary	ovary
31	chr7:50733400-50737000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr7:50733600-50738400	Strong transcription	A549	lung
33	chr7:50733600-50741800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr7:50733800-50742600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr7:50734000-50737200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:50734000-50737600	Weak transcription	K562	blood
37	chr7:50734200-50737400	Enhancers	Fetal Heart	heart
38	chr7:50734200-50743400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:50734200-50748800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr7:50734400-50736600	Enhancers	Lung	lung
41	chr7:50734400-50737000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr7:50734400-50740600	Weak transcription	Esophagus	oesophagus
43	chr7:50734400-50740800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr7:50734400-50742400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:50734600-50736200	Enhancers	NH-A	brain
46	chr7:50734600-50736600	Enhancers	Rectal Smooth Muscle	rectum
47	chr7:50734600-50736800	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr7:50734800-50736200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr7:50734800-50736200	Enhancers	Brain Cingulate Gyrus	brain
50	chr7:50734800-50736600	Enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links