Variant report

Variant	rs2237485
Chromosome Location	chr7:50749870-50749871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2072235	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2237467	0.84[EUR][1000 genomes]
rs2237468	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2237471	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2237472	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237473	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237477	0.80[ASN][1000 genomes]
rs2237478	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237479	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237483	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244347	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs2282930	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55830086	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs757999	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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
rs2237485	ABCA13	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50710000-50758200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:50731800-50750000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:50736600-50755200	Weak transcription	NHDF-Ad	bronchial
4	chr7:50738800-50765400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:50742000-50753000	Weak transcription	Osteobl	bone
6	chr7:50742200-50758200	Weak transcription	Brain Germinal Matrix	brain
7	chr7:50742200-50765200	Weak transcription	NHLF	lung
8	chr7:50742400-50753600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:50742400-50755000	Weak transcription	Esophagus	oesophagus
10	chr7:50742400-50755000	Weak transcription	NH-A	brain
11	chr7:50742400-50755200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr7:50742600-50757000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:50742600-50762200	Weak transcription	Hela-S3	cervix
14	chr7:50742600-50763000	Weak transcription	HSMM	muscle
15	chr7:50742600-50792000	Weak transcription	Primary T cells from cord blood	blood
16	chr7:50742800-50756200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr7:50742800-50757600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:50743000-50750200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr7:50743000-50750200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr7:50743000-50755000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr7:50743000-50755200	Weak transcription	K562	blood
22	chr7:50743000-50756400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr7:50743200-50754600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:50743400-50753000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:50743400-50754200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:50743800-50754600	Weak transcription	Fetal Brain Female	brain
27	chr7:50744400-50753800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr7:50745000-50754600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:50745400-50752000	Enhancers	Liver	Liver
30	chr7:50745600-50753000	Weak transcription	Aorta	Aorta
31	chr7:50745600-50753800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr7:50745600-50761200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:50745800-50754800	Weak transcription	Fetal Brain Male	brain
34	chr7:50745800-50755400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:50745800-50769600	Weak transcription	Gastric	stomach
36	chr7:50746000-50765200	Weak transcription	Stomach Mucosa	stomach
37	chr7:50746400-50758400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr7:50746600-50750400	Enhancers	Colon Smooth Muscle	Colon
39	chr7:50747000-50752200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:50747000-50753800	Weak transcription	HSMMtube	muscle
41	chr7:50747400-50750000	Enhancers	Stomach Smooth Muscle	stomach
42	chr7:50747400-50752200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr7:50747400-50753400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr7:50747600-50755200	Weak transcription	Ovary	ovary
45	chr7:50748000-50754600	Weak transcription	A549	lung
46	chr7:50748200-50750200	Enhancers	Pancreas	Pancrea
47	chr7:50748200-50758200	Weak transcription	Brain Anterior Caudate	brain
48	chr7:50748400-50750800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr7:50748600-50750000	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr7:50748600-50750200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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