Variant report

Variant	rs2282930
Chromosome Location	chr7:50754679-50754680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs17133984	0.89[AFR][1000 genomes]
rs2072235	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2108351	0.90[AFR][1000 genomes]
rs2158918	0.89[AFR][1000 genomes]
rs2237468	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2237471	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237472	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237473	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237478	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237479	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237483	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237485	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2244347	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs2529398	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2529401	1.00[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2529406	0.90[AFR][1000 genomes]
rs2715099	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2715101	0.90[AFR][1000 genomes]
rs2715106	0.90[AFR][1000 genomes]
rs2715122	0.90[AFR][1000 genomes]
rs2715124	0.90[AFR][1000 genomes]
rs2715136	0.90[AFR][1000 genomes]
rs2715137	0.90[AFR][1000 genomes]
rs55830086	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs757999	0.84[AMR][1000 genomes];0.92[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

Variant related diseases (count:1)

Disease	PMID	Source
Bone mineral density	22504420	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2282930	ABCA13	cis	cerebellum	SCAN

Chromatin state (count:91 , 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	chr7:50736600-50755200	Weak transcription	NHDF-Ad	bronchial
3	chr7:50738800-50765400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:50742200-50758200	Weak transcription	Brain Germinal Matrix	brain
5	chr7:50742200-50765200	Weak transcription	NHLF	lung
6	chr7:50742400-50755000	Weak transcription	Esophagus	oesophagus
7	chr7:50742400-50755000	Weak transcription	NH-A	brain
8	chr7:50742400-50755200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr7:50742600-50757000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr7:50742600-50762200	Weak transcription	Hela-S3	cervix
11	chr7:50742600-50763000	Weak transcription	HSMM	muscle
12	chr7:50742600-50792000	Weak transcription	Primary T cells from cord blood	blood
13	chr7:50742800-50756200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:50742800-50757600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:50743000-50755000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:50743000-50755200	Weak transcription	K562	blood
17	chr7:50743000-50756400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr7:50745600-50761200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:50745800-50754800	Weak transcription	Fetal Brain Male	brain
20	chr7:50745800-50755400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:50745800-50769600	Weak transcription	Gastric	stomach
22	chr7:50746000-50765200	Weak transcription	Stomach Mucosa	stomach
23	chr7:50746400-50758400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:50747600-50755200	Weak transcription	Ovary	ovary
25	chr7:50748200-50758200	Weak transcription	Brain Anterior Caudate	brain
26	chr7:50749800-50755400	Weak transcription	Fetal Heart	heart
27	chr7:50750000-50754800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr7:50750000-50756600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr7:50750000-50778600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr7:50750200-50754800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:50750200-50755000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr7:50750200-50755000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr7:50750200-50755000	Weak transcription	Spleen	Spleen
34	chr7:50750200-50755200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr7:50750200-50755200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr7:50750200-50758600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr7:50752200-50755200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr7:50752200-50756200	Enhancers	Rectal Smooth Muscle	rectum
39	chr7:50752200-50756600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr7:50752600-50755600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr7:50752600-50759800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr7:50752800-50755000	Weak transcription	Fetal Intestine Small	intestine
43	chr7:50752800-50756200	Enhancers	Fetal Muscle Leg	muscle
44	chr7:50752800-50756800	Enhancers	Left Ventricle	heart
45	chr7:50752800-50765200	Weak transcription	Fetal Intestine Large	intestine
46	chr7:50753000-50755000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr7:50753000-50757600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
48	chr7:50753200-50755200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr7:50753200-50756400	Enhancers	Colon Smooth Muscle	Colon
50	chr7:50753200-50757000	Enhancers	Psoas Muscle	Psoas

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