Variant report

Variant	rs11079797
Chromosome Location	chr17:45912302-45912303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:45911472-45912443	K562	blood:	n/a	n/a
2	POLR2A	chr17:45912165-45912508	HCT-116	colon:	n/a	n/a
3	POLR2A	chr17:45912255-45912801	HepG2	liver:	n/a	n/a

No data

(count:7 , 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	chr17:45910559..45913334-chr17:45936113..45939006,2	MCF-7	breast:
5	chr17:45912279..45914440-chr17:45926481..45928555,2	K562	blood:
6	chr17:45910473..45912367-chr17:46035358..46036860,2	MCF-7	breast:
7	chr17:45912193..45915082-chr17:46064625..46066503,2	MCF-7	breast:

No data

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

Extended variants
information (count: 30 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10428	0.83[ASW][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap]
rs11079798	0.82[EUR][1000 genomes]
rs11079799	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs11651698	0.83[EUR][1000 genomes]
rs16948424	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs16948662	1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs2010952	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2074185	0.89[GIH][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs4793688	0.82[JPT][hapmap]
rs4794202	0.84[EUR][1000 genomes]
rs4794204	0.82[EUR][1000 genomes]
rs4794224	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs59715174	0.86[EUR][1000 genomes]
rs62066132	0.82[EUR][1000 genomes]
rs6503875	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7212099	1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7214694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8078688	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs916798	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9895764	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9896712	0.85[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs9897598	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9903904	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9904503	0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9915028	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][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
rs11079797	SCRN2	cis	Adipose Subcutaneous	GTEx
rs11079797	C1QL1	cis	parietal	SCAN
rs11079797	SCRN2	cis	Whole Blood	GTEx
rs11079797	SCRN2	cis	lymphoblastoid	seeQTL
rs11079797	SCRN2	cis	Stomach	GTEx
rs11079797	SCRN2	cis	Esophagus Muscularis	GTEx
rs11079797	CNTNAP1	cis	cerebellum	SCAN
rs11079797	SCRN2	cis	lung	GTEx
rs11079797	OSBPL7	cis	cerebellum	SCAN
rs11079797	SCRN2	cis	Esophagus Mucosa	GTEx
rs11079797	SCRN2	cis	Muscle Skeletal	GTEx
rs11079797	SCRN2	cis	Skin Sun Exposed Lower leg	GTEx
rs11079797	LRRC46	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45909200-45912800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr17:45909200-45916800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:45909400-45912600	Weak transcription	HSMMtube	muscle
4	chr17:45909400-45913200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr17:45909400-45913200	Enhancers	Spleen	Spleen
6	chr17:45909400-45915800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr17:45909400-45917600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr17:45909600-45912600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr17:45909600-45912600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:45909600-45912600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr17:45909600-45912600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr17:45909600-45912600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr17:45909600-45912600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr17:45909600-45912600	Weak transcription	Gastric	stomach
15	chr17:45909600-45912600	Weak transcription	Right Ventricle	heart
16	chr17:45909600-45912800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:45909600-45912800	Weak transcription	Brain Germinal Matrix	brain
18	chr17:45909600-45912800	Weak transcription	Colonic Mucosa	Colon
19	chr17:45909600-45912800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr17:45909600-45913000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr17:45909600-45913000	Enhancers	Adipose Nuclei	Adipose
22	chr17:45909600-45913200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr17:45909600-45913200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr17:45909600-45913200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr17:45909600-45913200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr17:45909600-45913200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr17:45909600-45913200	Weak transcription	Esophagus	oesophagus
28	chr17:45909600-45913200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr17:45909600-45913200	Weak transcription	A549	lung
30	chr17:45909600-45913400	Weak transcription	Aorta	Aorta
31	chr17:45909600-45913400	Weak transcription	Ovary	ovary
32	chr17:45909600-45913400	Weak transcription	Pancreas	Pancrea
33	chr17:45909600-45913400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr17:45909600-45913400	Weak transcription	HSMM	muscle
35	chr17:45909600-45913400	Weak transcription	NHLF	lung
36	chr17:45909600-45914400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr17:45909600-45914400	Weak transcription	NH-A	brain
38	chr17:45909600-45915200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr17:45909600-45915400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr17:45909600-45917000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:45909600-45917000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr17:45909600-45917200	Weak transcription	Stomach Mucosa	stomach
43	chr17:45909600-45917400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr17:45909600-45917400	Weak transcription	Fetal Kidney	kidney
45	chr17:45909600-45917600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr17:45909600-45917600	Weak transcription	Psoas Muscle	Psoas
47	chr17:45909600-45917600	Weak transcription	Right Atrium	heart
48	chr17:45909800-45912400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr17:45909800-45912400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr17:45909800-45912400	Weak transcription	Fetal Intestine Small	intestine

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