Variant report

Variant	rs2666503
Chromosome Location	chr1:62736771-62736772
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10493320	0.82[AMR][1000 genomes]
rs12063531	0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs12078087	0.82[AMR][1000 genomes]
rs12079207	0.82[AMR][1000 genomes]
rs12122645	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs12718429	0.82[AMR][1000 genomes]
rs12760895	0.80[MEX][hapmap]
rs1555833	0.87[ASN][1000 genomes]
rs2258470	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2260581	0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2262106	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2262110	0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2457806	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2457808	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2457810	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2666472	0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2666473	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2666474	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2666475	0.86[ASN][1000 genomes]
rs2666476	0.86[ASN][1000 genomes]
rs2666482	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2666487	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2666488	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2666506	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2666507	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2666508	1.00[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2765241	0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2765244	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2765245	0.87[ASN][1000 genomes]
rs2765247	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2765248	0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2765249	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2765250	0.89[ASN][1000 genomes]
rs2765251	0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2765258	0.86[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2765270	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs34752481	0.88[AMR][1000 genomes]
rs7516290	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765692	0.82[MEX][hapmap]
rs912894	0.82[AMR][1000 genomes]
rs912895	0.82[AMR][1000 genomes]
rs912896	0.82[AMR][1000 genomes]
rs958803	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs982504	0.81[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2666503	DAB1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62711600-62737200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:62721000-62739400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:62729000-62737600	Weak transcription	Right Atrium	heart
4	chr1:62729600-62736800	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:62729600-62737400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:62729600-62737400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:62729600-62737600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:62729600-62737800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:62729800-62737400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:62732200-62737000	Weak transcription	Esophagus	oesophagus
11	chr1:62732200-62737600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:62732400-62737000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:62732400-62737400	Weak transcription	Fetal Kidney	kidney
14	chr1:62732400-62737600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:62732400-62737600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:62732400-62737600	Weak transcription	Placenta	Placenta
17	chr1:62732400-62740000	Weak transcription	Liver	Liver
18	chr1:62732400-62748400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:62732800-62737600	Weak transcription	Fetal Intestine Small	intestine
20	chr1:62733000-62741000	Weak transcription	Brain Germinal Matrix	brain
21	chr1:62733200-62737400	Weak transcription	Fetal Lung	lung
22	chr1:62734000-62737400	Weak transcription	Adipose Nuclei	Adipose
23	chr1:62734200-62750800	Weak transcription	Gastric	stomach
24	chr1:62734600-62736800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:62734800-62737400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:62734800-62737400	Weak transcription	Pancreas	Pancrea
27	chr1:62734800-62737600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:62735000-62736800	Weak transcription	Fetal Stomach	stomach
29	chr1:62735800-62740600	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr1:62736000-62737000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:62736200-62739600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:62736400-62738400	Enhancers	Fetal Heart	heart
33	chr1:62736400-62739400	Enhancers	Primary hematopoietic stem cells	blood
34	chr1:62736400-62739400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:62736400-62740400	Enhancers	Fetal Thymus	thymus
36	chr1:62736400-62741000	Strong transcription	HepG2	liver

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