Variant report

Variant	rs2457808
Chromosome Location	chr1:62716353-62716354
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12122645	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1806870	0.87[ASN][1000 genomes]
rs2258470	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2260581	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2262106	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2262110	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2457806	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2457810	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2457811	1.00[ASN][1000 genomes]
rs2666472	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2666473	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2666474	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs2666475	0.86[ASN][1000 genomes]
rs2666476	0.86[ASN][1000 genomes]
rs2666479	0.93[ASN][1000 genomes]
rs2666481	0.89[ASN][1000 genomes]
rs2666482	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2666503	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2765241	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2765244	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2765245	0.85[ASN][1000 genomes]
rs2765247	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2765248	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2765249	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2765250	0.83[ASN][1000 genomes]
rs2765270	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2774937	0.84[ASN][1000 genomes]
rs2774938	0.94[ASN][1000 genomes]
rs6421473	0.96[ASN][1000 genomes]
rs7516290	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7529326	0.99[ASN][1000 genomes]
rs958803	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9662717	0.99[ASN][1000 genomes]
rs982504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2457808	DAB1	cis	cerebellum	SCAN
rs2457808	NOD1	trans	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62704000-62720600	Weak transcription	Right Atrium	heart
2	chr1:62707600-62719600	Weak transcription	Fetal Kidney	kidney
3	chr1:62707600-62732000	Weak transcription	Gastric	stomach
4	chr1:62707800-62727400	Weak transcription	Pancreas	Pancrea
5	chr1:62708200-62720000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:62710800-62731800	Weak transcription	Fetal Intestine Small	intestine
7	chr1:62711400-62718000	Weak transcription	HepG2	liver
8	chr1:62711600-62730600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:62711600-62737200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:62712000-62727400	Weak transcription	Fetal Lung	lung
11	chr1:62712000-62731600	Weak transcription	Placenta	Placenta
12	chr1:62712200-62716400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:62713400-62728800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:62713800-62718000	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:62714000-62717800	Weak transcription	Fetal Heart	heart
16	chr1:62714200-62716400	Weak transcription	Adipose Nuclei	Adipose
17	chr1:62715400-62717000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr1:62715800-62716400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:62715800-62716800	Enhancers	Primary hematopoietic stem cells	blood
20	chr1:62715800-62716800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:62716200-62716800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:62716200-62719200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:62716200-62719600	Strong transcription	Fetal Stomach	stomach

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