Variant report

Variant	rs4072739
Chromosome Location	chr17:17884660-17884661
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	chr17:17874682..17878997-chr17:17883276..17886236,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TOM1L2-1	chr17:17884506-17884886	NONHSAT146127

Variant related genes	Relation type
ENSG00000171962	Chromatin interaction
ENSG00000175662	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs11078408	0.85[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs11650021	0.86[EUR][1000 genomes]
rs11869491	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11870660	0.85[CEU][hapmap];0.81[LWK][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs11871231	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12150369	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12939020	0.84[EUR][1000 genomes]
rs28537385	0.95[EUR][1000 genomes]
rs28555361	0.80[EUR][1000 genomes]
rs2955350	0.87[EUR][1000 genomes]
rs2955353	0.87[EUR][1000 genomes]
rs2955354	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2955355	0.94[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2955356	0.95[CEU][hapmap];0.85[GIH][hapmap];0.83[LWK][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes]
rs2955357	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2955358	0.94[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2955359	0.95[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs2955368	0.86[EUR][1000 genomes]
rs2955370	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2955372	0.95[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs2955377	0.90[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs2955378	0.95[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2955380	0.95[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2955381	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2955383	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2955384	0.95[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2955385	0.95[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2974999	0.89[CEU][hapmap]
rs4072738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4299203	0.85[CEU][hapmap];0.82[LWK][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs4365348	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4368210	0.95[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs4426402	0.89[CEU][hapmap]
rs4459604	0.89[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs4471742	0.81[EUR][1000 genomes]
rs4506969	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs4584886	0.95[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs4643387	0.84[EUR][1000 genomes]
rs4924832	0.94[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.98[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4925133	0.89[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925135	0.86[EUR][1000 genomes]
rs4925136	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs57728924	0.82[EUR][1000 genomes]
rs62072048	0.87[EUR][1000 genomes]
rs62072050	0.93[EUR][1000 genomes]
rs6502631	0.95[EUR][1000 genomes]
rs6502632	0.95[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6502633	0.88[EUR][1000 genomes]
rs6502634	0.83[EUR][1000 genomes]
rs6502636	0.94[CEU][hapmap]
rs7207461	0.87[EUR][1000 genomes]
rs7207821	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs7209003	0.95[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7210400	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7211714	0.89[CEU][hapmap]
rs7212167	0.95[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7212447	0.89[CEU][hapmap]
rs7215524	0.92[EUR][1000 genomes]
rs721669	0.89[CEU][hapmap]
rs7219320	0.86[LWK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs7219324	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7223696	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7224047	0.90[EUR][1000 genomes]
rs7406982	0.95[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs7503738	0.87[EUR][1000 genomes]
rs8068175	0.85[CEU][hapmap];0.82[LWK][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs8069811	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs8071238	0.87[EUR][1000 genomes]
rs8075189	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs8080602	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs8082590	0.81[EUR][1000 genomes]
rs854763	0.89[CEU][hapmap]
rs854767	0.89[CEU][hapmap]
rs854769	0.89[CEU][hapmap]
rs854790	0.89[CEU][hapmap]
rs854791	0.89[CEU][hapmap]
rs854809	0.89[CEU][hapmap]
rs854814	0.89[CEU][hapmap]
rs854817	0.89[CEU][hapmap]
rs9303144	0.89[CEU][hapmap]
rs9894138	0.87[EUR][1000 genomes]
rs9896837	0.95[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs9897761	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9899355	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9911850	0.95[EUR][1000 genomes]
rs9912096	0.96[EUR][1000 genomes]
rs9913277	0.89[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs9914127	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4072739	TOM1L2	cis	cerebellum	SCAN
rs4072739	TOM1L2	cis	parietal	SCAN
rs4072739	C17orf39	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17876400-17888600	Weak transcription	Lung	lung
2	chr17:17876400-17903200	Weak transcription	Gastric	stomach
3	chr17:17876600-17884800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr17:17876600-17914600	Weak transcription	Aorta	Aorta
5	chr17:17876800-17891800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr17:17876800-17909400	Weak transcription	Brain Substantia Nigra	brain
7	chr17:17876800-17912000	Weak transcription	Colon Smooth Muscle	Colon
8	chr17:17877000-17886400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr17:17877000-17886400	Weak transcription	NHEK	skin
10	chr17:17877000-17887000	Weak transcription	Brain Anterior Caudate	brain
11	chr17:17877000-17888000	Weak transcription	Ovary	ovary
12	chr17:17877000-17891000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:17877000-17891800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr17:17877000-17900000	Weak transcription	Fetal Intestine Small	intestine
15	chr17:17877200-17891200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr17:17877200-17891400	Weak transcription	Fetal Muscle Leg	muscle
17	chr17:17877600-17893200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr17:17880000-17885000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr17:17881600-17891200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr17:17881800-17908200	Weak transcription	Pancreas	Pancrea
21	chr17:17882600-17891800	Weak transcription	Spleen	Spleen
22	chr17:17883400-17886000	Weak transcription	Stomach Mucosa	stomach
23	chr17:17883400-17886600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr17:17883400-17888200	Weak transcription	Fetal Stomach	stomach
25	chr17:17883400-17893000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr17:17883600-17892600	Weak transcription	Esophagus	oesophagus
27	chr17:17884400-17884800	Enhancers	Brain Hippocampus Middle	brain
28	chr17:17884400-17885000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr17:17884600-17885000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr17:17884600-17885000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:17884600-17885000	Enhancers	Brain Angular Gyrus	brain
32	chr17:17884600-17885000	Enhancers	Brain Cingulate Gyrus	brain
33	chr17:17884600-17897400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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