Variant report

Variant	rs736929
Chromosome Location	chr14:97343323-97343324
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10131201	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10131630	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10145383	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10146571	1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10149107	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10873476	0.82[ASN][1000 genomes]
rs11160369	0.82[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11160371	0.91[ASN][1000 genomes]
rs11160375	0.82[ASN][1000 genomes]
rs11628733	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs12433112	0.90[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12434466	0.80[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs12435963	0.90[ASN][1000 genomes]
rs12589919	0.90[CHB][hapmap]
rs12590723	0.90[ASN][1000 genomes]
rs12878184	0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs12882853	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12894621	0.90[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs12897588	0.90[CHB][hapmap]
rs12897731	0.95[ASN][1000 genomes]
rs1951311	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1951312	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1957137	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2145636	0.90[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2180896	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2224442	0.82[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2230532	0.90[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3825576	0.89[ASN][1000 genomes]
rs4270096	0.90[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4900346	0.90[CHB][hapmap]
rs4900347	0.92[ASN][1000 genomes]
rs4900349	0.95[ASN][1000 genomes]
rs4900350	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs4900351	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4900353	1.00[CHB][hapmap]
rs4905546	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4905547	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4905548	0.90[CHB][hapmap]
rs4905551	1.00[CHB][hapmap]
rs4905552	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4905553	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4905555	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4905557	0.84[AMR][1000 genomes]
rs4905558	0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4905560	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4905564	0.82[ASN][1000 genomes]
rs4905568	0.84[ASN][1000 genomes]
rs58514314	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61981027	0.97[ASN][1000 genomes]
rs67804110	0.85[ASN][1000 genomes]
rs67957817	0.86[ASN][1000 genomes]
rs7141028	0.84[AMR][1000 genomes]
rs71419296	0.85[ASN][1000 genomes]
rs7156355	0.90[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs722869	0.84[ASN][1000 genomes]
rs723810	0.90[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs749279	1.00[CHB][hapmap]
rs764300	0.90[CHB][hapmap]
rs8013081	0.90[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs8016614	0.97[ASN][1000 genomes]
rs9285600	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9323951	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9323954	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9323955	0.90[CHB][hapmap];0.83[CHD][hapmap];0.82[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	nsv1044202	chr14:97155291-97683983	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv542179	chr14:97155291-97683983	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv948620	chr14:97334444-98133191	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs736929	VRK1	cis	cerebellum	SCAN
rs736929	VRK1	cis	parietal	SCAN
rs736929	KDM3A	trans	cerebellum	SCAN
rs736929	OTUB2	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:97294000-97362600	Weak transcription	Spleen	Spleen
2	chr14:97297600-97353400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr14:97298800-97348800	Strong transcription	Dnd41	blood
4	chr14:97298800-97350600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr14:97299400-97353600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr14:97303400-97371600	Weak transcription	Ovary	ovary
7	chr14:97308200-97348800	Weak transcription	Fetal Intestine Small	intestine
8	chr14:97309600-97344400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr14:97314800-97344000	Weak transcription	Fetal Muscle Leg	muscle
10	chr14:97314800-97347600	Weak transcription	Lung	lung
11	chr14:97314800-97355000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr14:97315600-97343800	Weak transcription	Left Ventricle	heart
13	chr14:97315600-97346600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr14:97315600-97350400	Weak transcription	NHDF-Ad	bronchial
15	chr14:97316000-97344400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr14:97321800-97343800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr14:97322000-97344600	Weak transcription	HUVEC	blood vessel
18	chr14:97322000-97348400	Weak transcription	HSMM	muscle
19	chr14:97322200-97354200	Weak transcription	Hela-S3	cervix
20	chr14:97323800-97354600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr14:97324000-97350800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr14:97324000-97352600	Weak transcription	HMEC	breast
23	chr14:97324200-97346400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr14:97324200-97348400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr14:97324200-97350600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr14:97324200-97354200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr14:97324400-97346000	Weak transcription	HepG2	liver
28	chr14:97324800-97346600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr14:97325200-97353800	Weak transcription	Fetal Lung	lung
30	chr14:97325200-97354600	Weak transcription	Thymus	Thymus
31	chr14:97325600-97362000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr14:97330400-97345200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr14:97331000-97378400	Weak transcription	A549	lung
34	chr14:97331400-97347200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr14:97331800-97346600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr14:97333000-97348800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr14:97337400-97354200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr14:97338400-97355200	Weak transcription	Psoas Muscle	Psoas
39	chr14:97338600-97348200	Weak transcription	Small Intestine	intestine
40	chr14:97339400-97344200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr14:97340000-97344200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr14:97340200-97344000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr14:97340200-97345000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr14:97340200-97350400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr14:97340400-97344400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr14:97340600-97343800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr14:97340800-97343600	Weak transcription	Aorta	Aorta
48	chr14:97340800-97346600	Weak transcription	Pancreas	Pancrea
49	chr14:97340800-97348200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr14:97340800-97348400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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