Variant report

Variant	rs2260581
Chromosome Location	chr1:62728861-62728862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12122645	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1806870	0.81[ASN][1000 genomes]
rs2258470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262110	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457806	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2457808	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2457810	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2457811	0.85[ASN][1000 genomes]
rs2666472	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666473	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666474	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666475	0.99[ASN][1000 genomes]
rs2666476	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2666479	0.80[ASN][1000 genomes]
rs2666482	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2666503	0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2666507	0.90[JPT][hapmap]
rs2666508	0.90[JPT][hapmap]
rs2765241	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765244	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765245	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765247	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765248	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765250	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2765251	0.86[JPT][hapmap]
rs2765270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6421473	0.81[ASN][1000 genomes]
rs7516290	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7529326	0.84[ASN][1000 genomes]
rs958803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9662717	0.84[ASN][1000 genomes]
rs982504	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2260581	DAB1	cis	cerebellum	SCAN
rs2260581	PDE4B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62707600-62732000	Weak transcription	Gastric	stomach
2	chr1:62710800-62731800	Weak transcription	Fetal Intestine Small	intestine
3	chr1:62711600-62730600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:62711600-62737200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:62712000-62731600	Weak transcription	Placenta	Placenta
6	chr1:62721000-62739400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:62727400-62729400	Enhancers	Pancreas	Pancrea
8	chr1:62727600-62729000	Strong transcription	Placenta Amnion	Placenta Amnion
9	chr1:62727800-62729600	Strong transcription	HepG2	liver
10	chr1:62728000-62734800	Weak transcription	Fetal Brain Male	brain
11	chr1:62728200-62729000	Weak transcription	Fetal Lung	lung
12	chr1:62728400-62729400	Strong transcription	Liver	Liver
13	chr1:62728600-62729200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:62728600-62729200	Genic enhancers	Fetal Muscle Trunk	muscle
15	chr1:62728600-62729600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:62728600-62729600	Enhancers	Fetal Heart	heart
17	chr1:62728600-62732000	Weak transcription	Fetal Kidney	kidney
18	chr1:62728800-62729000	ZNF genes & repeats	Right Atrium	heart
19	chr1:62728800-62729200	Enhancers	H1 Cell Line	embryonic stem cell
20	chr1:62728800-62729200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:62728800-62729200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:62728800-62729200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:62728800-62729200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:62728800-62729400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:62728800-62729400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr1:62728800-62729400	Enhancers	Spleen	Spleen
27	chr1:62728800-62729600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:62728800-62729600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:62728800-62729600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr1:62728800-62729600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr1:62728800-62729600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:62728800-62729600	Enhancers	Adipose Nuclei	Adipose
33	chr1:62728800-62729600	Enhancers	Fetal Muscle Leg	muscle
34	chr1:62728800-62729800	Enhancers	H9 Cell Line	embryonic stem cell
35	chr1:62728800-62730000	Genic enhancers	Fetal Stomach	stomach
36	chr1:62728800-62730400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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