Variant report

Variant	rs6968827
Chromosome Location	chr7:50802434-50802435
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	chr7:50801886-50803151	K562	blood:	n/a	n/a

Variant related genes	Relation type
GRB10	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1024529	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10272063	0.80[AMR][1000 genomes]
rs10273302	0.80[CEU][hapmap]
rs10278363	0.88[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs11238339	0.81[CEU][hapmap]
rs12536500	0.94[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12665949	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs13236710	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs17134002	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17152120	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs1962390	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1962391	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1978208	0.82[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2329424	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2329490	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329491	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2329494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2529399	0.91[ASN][1000 genomes]
rs2715119	0.82[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3779072	0.82[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4947828	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947861	0.88[CEU][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs6593145	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6593182	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs7383871	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780348	0.82[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782797	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7794299	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6968827	FIGNL1	cis	cerebellum	SCAN
rs6968827	VWC2	cis	cerebellum	SCAN
rs6968827	VSTM2A	cis	cerebellum	SCAN
rs6968827	LOC100129427	cis	parietal	SCAN
rs6968827	C7orf72	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50763400-50806800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:50773000-50807400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:50780600-50807600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:50787000-50807600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr7:50788000-50816000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:50789400-50811600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr7:50789600-50807400	Weak transcription	Esophagus	oesophagus
8	chr7:50793200-50807200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr7:50793800-50807200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr7:50794800-50803000	Weak transcription	Primary T cells from cord blood	blood
11	chr7:50795200-50807400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:50798000-50812000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:50798600-50822600	Weak transcription	Ovary	ovary
14	chr7:50798800-50806800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:50798800-50807400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:50798800-50810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:50798800-50811400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:50798800-50815200	Weak transcription	Aorta	Aorta
19	chr7:50798800-50815200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr7:50798800-50824800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:50798800-50832400	Weak transcription	HSMM	muscle
22	chr7:50798800-50837200	Weak transcription	HSMMtube	muscle
23	chr7:50799000-50804600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:50799000-50807200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:50799000-50815200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr7:50799000-50817400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr7:50799000-50823000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr7:50799200-50807200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr7:50799200-50807400	Weak transcription	Fetal Lung	lung
30	chr7:50799200-50811400	Weak transcription	Fetal Brain Female	brain
31	chr7:50799800-50805600	Weak transcription	K562	blood
32	chr7:50799800-50807200	Weak transcription	Brain Substantia Nigra	brain
33	chr7:50800000-50804200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr7:50800000-50806200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:50800000-50807000	Weak transcription	HUVEC	blood vessel
36	chr7:50800400-50803000	Weak transcription	Brain Germinal Matrix	brain
37	chr7:50800400-50811200	Weak transcription	Fetal Stomach	stomach
38	chr7:50801000-50802600	Enhancers	NH-A	brain
39	chr7:50801000-50802800	Enhancers	Stomach Mucosa	stomach
40	chr7:50801200-50802600	Enhancers	Hela-S3	cervix
41	chr7:50801400-50805600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr7:50801600-50802600	Enhancers	A549	lung
43	chr7:50801600-50806000	Weak transcription	HepG2	liver
44	chr7:50801600-50806800	Weak transcription	Colon Smooth Muscle	Colon
45	chr7:50801600-50807200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:50801600-50807600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr7:50801600-50811400	Weak transcription	Osteobl	bone
48	chr7:50801600-50814400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr7:50801800-50802800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:50801800-50803200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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