Variant report

Variant	rs1014384
Chromosome Location	chr7:50847646-50847647
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:50847233-50848628	A549	lung:	n/a	n/a

Variant related genes	Relation type
GRB10	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1015573	0.81[ASN][1000 genomes]
rs1019000	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs10226937	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10231012	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10235345	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10239268	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1024531	0.82[AMR][1000 genomes]
rs10248029	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10258458	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10264904	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10268643	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10273302	0.82[CEU][hapmap];0.85[JPT][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10276986	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10281065	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10464765	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10464766	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10464790	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10486761	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11238310	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11238311	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11238313	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11238315	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11238325	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11238326	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11238337	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11238339	0.82[CEU][hapmap];0.85[JPT][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11763072	0.85[JPT][hapmap]
rs11974751	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978750	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11983539	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665949	0.82[CEU][hapmap]
rs12671577	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12674028	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12718925	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12718926	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12718927	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12718929	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12718930	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13232029	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13311390	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs1859571	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051895	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2051896	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074719	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2074720	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2074721	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2074722	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2074777	0.85[JPT][hapmap]
rs2158670	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286152	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2286154	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2329554	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2876846	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3801000	0.82[AMR][1000 genomes]
rs6593164	0.86[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6593173	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6593174	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6593180	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593200	0.89[ASN][1000 genomes]
rs6943153	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs6943901	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6945597	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6946194	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6951356	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6957007	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6958750	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960912	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6963498	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6966774	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6971834	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6979369	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs734422	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs757773	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs757774	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs757777	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs757778	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7785908	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7785914	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7786917	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7788511	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7791286	0.81[GIH][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs7793570	0.84[JPT][hapmap]
rs7802338	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7803278	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886700	0.84[AMR][1000 genomes];0.85[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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv824091	chr7:50828682-50885984	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538835	chr7:50839656-50867735	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv824092	chr7:50846084-50865531	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1014384	VWC2	cis	cerebellum	SCAN
rs1014384	LOC100129427	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50816200-50849600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr7:50822000-50849800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr7:50822800-50850200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:50823600-50849200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:50823600-50849200	Weak transcription	Fetal Lung	lung
6	chr7:50826600-50848400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr7:50829800-50849400	Weak transcription	Osteobl	bone
8	chr7:50830400-50848400	Weak transcription	Primary T cells from cord blood	blood
9	chr7:50833200-50850200	Weak transcription	HSMM	muscle
10	chr7:50833400-50848000	Weak transcription	Fetal Brain Female	brain
11	chr7:50835200-50847800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:50835200-50848200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr7:50835200-50849000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:50835400-50848200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr7:50835400-50849000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:50835800-50849800	Weak transcription	HUVEC	blood vessel
17	chr7:50836000-50849000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:50837800-50849800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr7:50838000-50850200	Weak transcription	HSMMtube	muscle
20	chr7:50838400-50848400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr7:50838400-50849200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:50838800-50849400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr7:50839200-50850200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:50839400-50848800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr7:50839800-50848800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr7:50839800-50850800	Weak transcription	Fetal Heart	heart
27	chr7:50840200-50848800	Weak transcription	Brain Germinal Matrix	brain
28	chr7:50843200-50847800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:50843600-50848400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr7:50843600-50849000	Weak transcription	Ovary	ovary
31	chr7:50843600-50849800	Weak transcription	Aorta	Aorta
32	chr7:50843800-50848000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr7:50843800-50848000	Weak transcription	Fetal Stomach	stomach
34	chr7:50843800-50848600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr7:50843800-50848800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr7:50843800-50848800	Weak transcription	Spleen	Spleen
37	chr7:50844000-50848200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr7:50844000-50848200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr7:50844000-50848400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr7:50844000-50848600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr7:50844000-50848600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr7:50844000-50848800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr7:50844400-50848600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr7:50844600-50848000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr7:50845000-50851600	Weak transcription	K562	blood
46	chr7:50845600-50848600	Enhancers	HepG2	liver
47	chr7:50845600-50850200	Enhancers	Liver	Liver
48	chr7:50845800-50848400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr7:50846000-50849000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:50846000-50849000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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