Variant report

Variant	rs12712063
Chromosome Location	chr2:100663281-100663282
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10209110	0.96[ASN][1000 genomes]
rs10211595	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10496344	0.81[CEU][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs1062143	0.97[ASN][1000 genomes]
rs11123804	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11123805	0.93[ASN][1000 genomes]
rs11123810	0.81[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs11123812	0.81[CEU][hapmap]
rs1115910	0.95[ASN][1000 genomes]
rs11681737	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11681966	0.81[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs11690905	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs12712062	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12995420	0.93[ASN][1000 genomes]
rs12997584	0.93[ASN][1000 genomes]
rs13003982	0.85[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs13415583	0.81[CEU][hapmap]
rs1370356	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1821828	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1821829	0.86[ASN][1000 genomes]
rs2309748	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2576678	0.93[ASN][1000 genomes]
rs2871326	0.97[ASN][1000 genomes]
rs4850921	0.81[CEU][hapmap]
rs6542905	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6714788	0.94[ASN][1000 genomes]
rs6733895	0.99[ASN][1000 genomes]
rs6750720	0.89[ASN][1000 genomes]
rs6754099	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7558817	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7582731	0.94[ASN][1000 genomes]
rs7599083	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7605430	0.95[ASN][1000 genomes]
rs9308833	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs961788	0.94[ASN][1000 genomes]

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	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12712063	MGAT4A	cis	parietal	SCAN
rs12712063	FER1L5	cis	parietal	SCAN
rs12712063	MRPL30	cis	cerebellum	SCAN
rs12712063	AFF3	cis	parietal	SCAN
rs12712063	COX5B	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100644600-100668400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr2:100648200-100666800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:100653200-100667200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:100654800-100668200	Weak transcription	Thymus	Thymus
5	chr2:100656400-100680000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:100656600-100686600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:100657800-100664400	Enhancers	Fetal Brain Male	brain
8	chr2:100658800-100668400	Weak transcription	Brain Germinal Matrix	brain
9	chr2:100659400-100680000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:100659600-100666000	Strong transcription	Primary B cells from cord blood	blood
11	chr2:100659800-100671600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:100660000-100669000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr2:100660600-100678200	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:100660800-100668800	Weak transcription	Lung	lung
15	chr2:100661600-100668800	Weak transcription	Fetal Brain Female	brain
16	chr2:100661800-100667200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:100661800-100668400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:100661800-100670400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:100662200-100684800	Weak transcription	Ovary	ovary
20	chr2:100662400-100663400	Strong transcription	Primary T cells from cord blood	blood
21	chr2:100662800-100664400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:100662800-100665600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr2:100662800-100667400	Weak transcription	Dnd41	blood
24	chr2:100662800-100674200	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:100663000-100663600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:100663000-100670400	Weak transcription	Gastric	stomach
27	chr2:100663000-100680800	Weak transcription	Fetal Kidney	kidney
28	chr2:100663000-100682200	Weak transcription	Fetal Heart	heart
29	chr2:100663200-100663600	Weak transcription	Fetal Lung	lung

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