Variant report

Variant	rs2627651
Chromosome Location	chr4:79382893-79382894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10001798	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10001918	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10018235	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10026662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1006079	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1027444	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11730871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13106736	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1484331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1484342	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1484343	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1496581	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1496582	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1496583	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1496584	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17003266	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2035511	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054721	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2054722	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2627648	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2627649	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2627650	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2627653	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2627654	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2627655	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2627656	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2645143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2645144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2645145	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2645146	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2645147	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2645148	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2645149	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28522970	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28566963	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2867068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2903470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34840208	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36095733	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3762844	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3899004	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4975065	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975067	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62308116	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6816851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs753751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs753752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7674053	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7699000	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs924149	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs949507	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs959539	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];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	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2627651	PAQR3	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79320000-79400200	Weak transcription	Psoas Muscle	Psoas
2	chr4:79333200-79391000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr4:79343200-79431800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:79354000-79391000	Weak transcription	Left Ventricle	heart
5	chr4:79354000-79401600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:79354200-79391000	Weak transcription	Fetal Kidney	kidney
7	chr4:79354400-79385200	Weak transcription	Pancreas	Pancrea
8	chr4:79363200-79409800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:79363400-79455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:79363800-79464200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:79365600-79406400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr4:79365800-79388200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:79366200-79408200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:79367200-79385400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:79368000-79385600	Weak transcription	Aorta	Aorta
16	chr4:79369400-79397800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:79372600-79395000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:79373600-79385400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:79374000-79397600	Weak transcription	Fetal Lung	lung
20	chr4:79374200-79398800	Weak transcription	Esophagus	oesophagus
21	chr4:79374600-79391000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:79375800-79391000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:79376000-79385200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:79376200-79387400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:79376200-79390000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr4:79376200-79398600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:79376200-79411600	Weak transcription	Fetal Stomach	stomach
28	chr4:79377000-79396200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:79378400-79383200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:79378600-79385400	Weak transcription	Fetal Intestine Small	intestine
31	chr4:79378600-79455800	Weak transcription	Right Ventricle	heart
32	chr4:79378800-79395800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:79379000-79385000	Weak transcription	HepG2	liver
34	chr4:79379200-79385200	Weak transcription	HSMMtube	muscle
35	chr4:79379400-79387200	Weak transcription	Fetal Intestine Large	intestine
36	chr4:79379600-79386200	Weak transcription	Fetal Heart	heart
37	chr4:79379600-79389400	Weak transcription	Brain Angular Gyrus	brain
38	chr4:79379800-79393200	Weak transcription	Brain Anterior Caudate	brain
39	chr4:79380800-79389600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:79381600-79385200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:79382000-79384600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr4:79382000-79384600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr4:79382200-79384600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr4:79382800-79384800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:79382800-79384800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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