Variant report

Variant	rs8076163
Chromosome Location	chr17:46120325-46120326
allele	C/T
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	chr17:46120283-46121360	K562	blood:	n/a	n/a
2	MAX	chr17:46120230-46120534	K562	blood:	n/a	chr17:46120262-46120271
3	POLR2A	chr17:46120258-46121281	Hela-S3	cervix:	n/a	n/a
4	BHLHE40	chr17:46120289-46120569	HepG2	liver:	n/a	n/a
5	BHLHE40	chr17:46120324-46120538	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46117511..46121845-chr17:46183690..46186313,3	MCF-7	breast:

Variant related genes	Relation type
COPZ2	TF binding region
ENSG00000002919	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10514935	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs12600464	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs12600478	0.86[JPT][hapmap]
rs1317850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240123	0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2256020	0.82[CEU][hapmap]
rs2938484	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs2957935	0.82[JPT][hapmap]
rs4794401	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7216411	0.91[CEU][hapmap];0.89[TSI][hapmap]
rs757352	1.00[CEU][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8076163	C17orf46	cis	parietal	SCAN
rs8076163	NFE2L1	cis	cerebellum	SCAN
rs8076163	ATP6V0A1	cis	parietal	SCAN
rs8076163	DNAJC7	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46114600-46120400	Weak transcription	K562	blood
2	chr17:46115600-46120400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr17:46115600-46120400	Weak transcription	Psoas Muscle	Psoas
4	chr17:46115600-46123800	Weak transcription	Brain Substantia Nigra	brain
5	chr17:46115800-46120400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr17:46115800-46120400	Weak transcription	HMEC	breast
7	chr17:46115800-46120400	Weak transcription	HSMMtube	muscle
8	chr17:46115800-46120600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:46115800-46122600	Weak transcription	Esophagus	oesophagus
10	chr17:46115800-46122800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr17:46115800-46122800	Weak transcription	Brain Anterior Caudate	brain
12	chr17:46115800-46122800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr17:46115800-46123200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr17:46115800-46123200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr17:46116000-46120400	Weak transcription	HSMM	muscle
16	chr17:46116000-46120400	Weak transcription	Osteobl	bone
17	chr17:46116000-46122600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:46116000-46122600	Weak transcription	NH-A	brain
19	chr17:46116000-46123000	Weak transcription	NHLF	lung
20	chr17:46116000-46124000	Weak transcription	Brain Hippocampus Middle	brain
21	chr17:46116200-46120400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr17:46117000-46122600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr17:46119200-46121400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr17:46119400-46123400	Weak transcription	A549	lung
25	chr17:46119400-46123800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr17:46120200-46120400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr17:46120200-46121400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr17:46120200-46121400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr17:46120200-46121400	Enhancers	NHEK	skin
30	chr17:46120200-46121600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr17:46120200-46121800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr17:46120200-46122600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr17:46120200-46122800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr17:46120200-46123000	Enhancers	NHDF-Ad	bronchial

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