Variant report

Variant	rs1019000
Chromosome Location	chr7:50809771-50809772
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	chr7:50790851..50793423-chr7:50808452..50810268,2	K562	blood:
2	chr7:50804663..50812652-chr7:50812790..50817860,10	K562	blood:

Variant related genes	Relation type
ENSG00000106070	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1014384	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs10226937	0.86[AMR][1000 genomes]
rs10231012	0.82[AMR][1000 genomes]
rs1024531	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10248029	0.86[AMR][1000 genomes]
rs10258458	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10264904	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10265504	0.80[ASN][1000 genomes]
rs10268643	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10281065	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10464765	0.81[AMR][1000 genomes]
rs10464766	0.81[AMR][1000 genomes]
rs10464790	0.81[AMR][1000 genomes]
rs10486761	0.89[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11238297	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11238310	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11238311	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11238313	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11238315	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11238325	0.86[AMR][1000 genomes]
rs11238326	0.84[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes]
rs11238337	0.84[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes]
rs11763072	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11763778	0.92[ASN][1000 genomes]
rs11765762	0.92[ASN][1000 genomes]
rs11974751	0.86[AMR][1000 genomes]
rs11983539	0.84[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs12536500	0.84[CEU][hapmap]
rs12668316	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12671577	0.86[AMR][1000 genomes]
rs12674028	0.86[AMR][1000 genomes]
rs12718925	0.81[AMR][1000 genomes]
rs12718926	0.81[AMR][1000 genomes]
rs12718927	0.84[AMR][1000 genomes]
rs12718929	0.81[AMR][1000 genomes]
rs12718930	0.81[AMR][1000 genomes]
rs13232029	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13311390	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.92[ASN][1000 genomes]
rs17134002	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs1859571	0.83[AMR][1000 genomes]
rs2051895	0.84[AMR][1000 genomes]
rs2051896	0.83[AMR][1000 genomes]
rs2058014	0.88[ASN][1000 genomes]
rs2074719	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2074720	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2074721	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2074722	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2074777	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2108349	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2190502	0.88[ASN][1000 genomes]
rs2214963	0.88[ASN][1000 genomes]
rs2237490	0.82[ASN][1000 genomes]
rs2286152	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2286154	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2299153	0.88[ASN][1000 genomes]
rs2329489	0.88[ASN][1000 genomes]
rs2329554	0.82[AMR][1000 genomes]
rs2876846	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3801000	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4521715	0.93[CHB][hapmap];0.88[ASN][1000 genomes]
rs4947806	0.92[ASN][1000 genomes]
rs6593164	0.89[CEU][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6593173	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6593174	0.89[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6593180	0.83[AMR][1000 genomes]
rs6943153	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6943901	0.84[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap]
rs6945597	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6946194	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6951356	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6957007	0.81[AMR][1000 genomes]
rs6958750	0.83[AMR][1000 genomes]
rs6960912	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6963498	0.84[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes]
rs6966774	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6967612	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6971834	0.84[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap]
rs6979369	0.88[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs734422	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs757773	0.89[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs757774	0.89[CEU][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7785908	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7785914	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7786917	0.84[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes]
rs7793570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7803278	0.83[AMR][1000 genomes]
rs7809623	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7809775	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs886700	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs933360	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1031138	chr7:50651793-50814881	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1019000	VWC2	cis	cerebellum	SCAN
rs1019000	LOC100129427	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50788000-50816000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr7:50789400-50811600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr7:50798000-50812000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:50798600-50822600	Weak transcription	Ovary	ovary
5	chr7:50798800-50810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:50798800-50811400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:50798800-50815200	Weak transcription	Aorta	Aorta
8	chr7:50798800-50815200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr7:50798800-50824800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:50798800-50832400	Weak transcription	HSMM	muscle
11	chr7:50798800-50837200	Weak transcription	HSMMtube	muscle
12	chr7:50799000-50815200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr7:50799000-50817400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr7:50799000-50823000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:50799200-50811400	Weak transcription	Fetal Brain Female	brain
16	chr7:50800400-50811200	Weak transcription	Fetal Stomach	stomach
17	chr7:50801600-50811400	Weak transcription	Osteobl	bone
18	chr7:50801600-50814400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr7:50802000-50810600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr7:50802000-50811200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:50802000-50814200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:50802200-50810000	Weak transcription	Fetal Intestine Large	intestine
23	chr7:50802200-50811200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:50802200-50815600	Weak transcription	Placenta	Placenta
25	chr7:50802600-50813200	Weak transcription	Hela-S3	cervix
26	chr7:50802600-50824000	Weak transcription	NH-A	brain
27	chr7:50802800-50814400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:50804600-50811600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr7:50806400-50811800	Weak transcription	K562	blood
30	chr7:50807600-50821800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr7:50807800-50821800	Weak transcription	Esophagus	oesophagus
32	chr7:50807800-50834800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr7:50808000-50810000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr7:50808000-50810000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr7:50808000-50810000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr7:50808000-50810000	Weak transcription	Fetal Thymus	thymus
37	chr7:50808000-50810000	Weak transcription	Psoas Muscle	Psoas
38	chr7:50808000-50810200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:50808000-50810600	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr7:50808000-50810600	Weak transcription	Brain Substantia Nigra	brain
41	chr7:50808000-50810600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr7:50808000-50811200	Weak transcription	Lung	lung
43	chr7:50808000-50811200	Weak transcription	Spleen	Spleen
44	chr7:50808000-50811400	Weak transcription	Adipose Nuclei	Adipose
45	chr7:50808000-50811400	Weak transcription	Right Atrium	heart
46	chr7:50808000-50811600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr7:50808000-50813600	Weak transcription	Right Ventricle	heart
48	chr7:50808000-50813800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:50808000-50814400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr7:50808000-50814400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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