Variant report

Variant	rs723810
Chromosome Location	chr14:97287970-97287971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:97263470..97265371-chr14:97287490..97290229,2	K562	blood:

Variant related genes	Relation type
ENSG00000100749	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10131201	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10131630	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10135234	0.81[CHD][hapmap]
rs10135283	0.81[CHD][hapmap]
rs10145383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10146571	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10149107	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873476	0.82[ASN][1000 genomes]
rs11160369	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11160371	0.91[ASN][1000 genomes]
rs11160375	0.82[ASN][1000 genomes]
rs11628733	0.91[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs12433112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12434466	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12435963	0.90[ASN][1000 genomes]
rs12589919	0.81[CHB][hapmap]
rs12590723	0.90[ASN][1000 genomes]
rs12878184	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs12882853	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12894621	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs12897588	1.00[CHB][hapmap]
rs12897731	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1951311	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951312	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1957137	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2145636	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2180896	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224442	0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2230532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825576	0.91[ASN][1000 genomes]
rs4270096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4900346	1.00[CHB][hapmap]
rs4900347	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4900349	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4900350	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4900351	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4900353	0.90[CHB][hapmap]
rs4905546	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4905547	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4905548	1.00[CHB][hapmap]
rs4905551	1.00[CHB][hapmap]
rs4905552	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4905553	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4905555	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4905557	1.00[CEU][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4905558	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4905560	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4905564	0.82[ASN][1000 genomes]
rs4905568	0.84[ASN][1000 genomes]
rs58514314	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61981027	1.00[ASN][1000 genomes]
rs67804110	0.87[ASN][1000 genomes]
rs67957817	0.86[ASN][1000 genomes]
rs7141028	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71419296	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7156355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs722869	0.86[ASN][1000 genomes]
rs736929	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	0.90[CHB][hapmap]
rs764300	1.00[CHB][hapmap]
rs8013081	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8016614	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9285600	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9323951	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9323954	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323955	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv510650	chr14:97238489-97325221	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1052138	chr14:97271794-97322583	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv542180	chr14:97271794-97322583	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1043916	chr14:97275088-97320354	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1051182	chr14:97275088-97337039	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs723810	VRK1	cis	parietal	SCAN
rs723810	VRK1	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:97264800-97288000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr14:97264800-97321600	Weak transcription	Psoas Muscle	Psoas
3	chr14:97265200-97293200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr14:97265600-97291800	Weak transcription	A549	lung
5	chr14:97266200-97303200	Weak transcription	Hela-S3	cervix
6	chr14:97271600-97313800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr14:97272400-97293800	Weak transcription	Primary B cells from cord blood	blood
8	chr14:97279600-97289200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr14:97279600-97289200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr14:97281400-97299800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr14:97282600-97293200	Weak transcription	Dnd41	blood
12	chr14:97282600-97300200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr14:97282800-97301800	Weak transcription	Thymus	Thymus
14	chr14:97283000-97288000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr14:97283000-97293200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr14:97283000-97293400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr14:97283000-97299800	Weak transcription	Fetal Thymus	thymus
18	chr14:97283000-97300800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr14:97283400-97292200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr14:97283400-97294200	Weak transcription	Primary T cells from cord blood	blood
21	chr14:97284600-97289200	Weak transcription	HepG2	liver
22	chr14:97284600-97289600	Weak transcription	K562	blood
23	chr14:97284600-97290600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr14:97284600-97291400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr14:97284600-97299000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr14:97284600-97313800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr14:97285400-97290600	Weak transcription	Osteobl	bone
28	chr14:97286200-97288000	Weak transcription	Aorta	Aorta
29	chr14:97286400-97290200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr14:97286800-97298800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr14:97287000-97288200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr14:97287000-97301600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr14:97287200-97288200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr14:97287200-97288200	Enhancers	Brain Germinal Matrix	brain
35	chr14:97287200-97288200	Enhancers	Fetal Brain Female	brain
36	chr14:97287200-97288600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr14:97287200-97288600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:97287200-97289400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr14:97287200-97289400	Enhancers	NHEK	skin
40	chr14:97287400-97288000	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr14:97287400-97288200	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr14:97287400-97288200	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr14:97287400-97288200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr14:97287400-97288200	Enhancers	Brain Anterior Caudate	brain
45	chr14:97287400-97288200	Enhancers	Brain Hippocampus Middle	brain
46	chr14:97287400-97289200	Enhancers	Fetal Brain Male	brain
47	chr14:97287600-97288000	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr14:97287600-97288200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr14:97287600-97288400	Flanking Active TSS	HMEC	breast
50	chr14:97287800-97288200	Enhancers	Brain Cingulate Gyrus	brain

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