Variant report

Variant	rs16948662
Chromosome Location	chr17:45913847-45913848
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:45912993-45913976	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45912259..45914443-chr17:45925886..45928377,3	MCF-7	breast:
2	chr17:45906958..45911258-chr17:45911981..45915187,7	K562	blood:
3	chr17:45911708..45914509-chr17:45972435..45974473,2	MCF-7	breast:
4	chr17:45912810..45915446-chr17:46033919..46035588,2	MCF-7	breast:
5	chr17:45913355..45915258-chr17:46023188..46024745,2	MCF-7	breast:
6	chr17:45912279..45914440-chr17:45926481..45928555,2	K562	blood:
7	chr17:45913357..45915949-chr17:45973586..45976163,2	K562	blood:
8	chr17:45912193..45915082-chr17:46064625..46066503,2	MCF-7	breast:
9	chr17:45913484..45922782-chr17:45969196..45975741,24	MCF-7	breast:

No data

Variant related genes	Relation type
MRPL10	TF binding region
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000141294	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10428	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs11079797	1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs11079799	0.82[JPT][hapmap]
rs16948424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2010952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2074185	0.82[JPT][hapmap]
rs34156395	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4793688	0.82[JPT][hapmap]
rs4794224	0.82[JPT][hapmap]
rs59111282	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62076102	0.90[ASN][1000 genomes]
rs62076106	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6503875	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7212099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214694	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs8078688	0.98[EUR][1000 genomes]
rs916798	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9895764	0.98[EUR][1000 genomes]
rs9896712	0.86[CEU][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs9897598	0.98[EUR][1000 genomes]
rs9904503	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs9915028	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv908574	chr17:45876022-45930584	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv517880	chr17:45887951-45933341	Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs16948662	SCRN2	cis	Esophagus Muscularis	GTEx
rs16948662	CNTNAP1	cis	cerebellum	SCAN
rs16948662	SCRN2	cis	Whole Blood	GTEx
rs16948662	KRTAP4-1	cis	cerebellum	SCAN
rs16948662	LRRC46	cis	lymphoblastoid	seeQTL
rs16948662	SCRN2	cis	Muscle Skeletal	GTEx
rs16948662	CALCOCO2	cis	cerebellum	SCAN
rs16948662	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs16948662	SCRN2	cis	Esophagus Mucosa	GTEx
rs16948662	SCRN2	cis	lymphoblastoid	seeQTL
rs16948662	SCRN2	cis	Adipose Subcutaneous	GTEx
rs16948662	SCRN2	cis	Skin Sun Exposed Lower leg	GTEx
rs16948662	SCRN2	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45909200-45916800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:45909400-45915800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr17:45909400-45917600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr17:45909600-45914400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr17:45909600-45914400	Weak transcription	NH-A	brain
6	chr17:45909600-45915200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr17:45909600-45915400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr17:45909600-45917000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:45909600-45917000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr17:45909600-45917200	Weak transcription	Stomach Mucosa	stomach
11	chr17:45909600-45917400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr17:45909600-45917400	Weak transcription	Fetal Kidney	kidney
13	chr17:45909600-45917600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr17:45909600-45917600	Weak transcription	Psoas Muscle	Psoas
15	chr17:45909600-45917600	Weak transcription	Right Atrium	heart
16	chr17:45909800-45914200	Weak transcription	HMEC	breast
17	chr17:45909800-45914400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:45909800-45914400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr17:45909800-45914400	Weak transcription	HepG2	liver
20	chr17:45909800-45914800	Weak transcription	NHDF-Ad	bronchial
21	chr17:45909800-45915800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:45909800-45916600	Weak transcription	Fetal Heart	heart
23	chr17:45909800-45917400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr17:45909800-45917400	Weak transcription	Brain Angular Gyrus	brain
25	chr17:45909800-45917400	Weak transcription	Brain Substantia Nigra	brain
26	chr17:45909800-45917400	Weak transcription	Hela-S3	cervix
27	chr17:45910000-45914600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr17:45910000-45915600	Weak transcription	Dnd41	blood
29	chr17:45910000-45917400	Weak transcription	Primary B cells from cord blood	blood
30	chr17:45910000-45917400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr17:45910000-45917400	Weak transcription	GM12878-XiMat	blood
32	chr17:45912200-45914400	Strong transcription	Fetal Intestine Large	intestine
33	chr17:45912200-45914600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr17:45912400-45914000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr17:45912400-45914000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr17:45912400-45914600	Strong transcription	Fetal Intestine Small	intestine
37	chr17:45912400-45917600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr17:45912600-45914000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr17:45912600-45914200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr17:45912600-45914800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr17:45912600-45914800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr17:45912600-45916200	Strong transcription	Gastric	stomach
43	chr17:45912600-45916800	Genic enhancers	Placenta	Placenta
44	chr17:45912600-45917000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr17:45912600-45917000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr17:45912600-45917600	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr17:45912800-45914000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr17:45912800-45914800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr17:45912800-45915000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:45912800-45915200	Strong transcription	Colonic Mucosa	Colon

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