Variant report

Variant	rs7224617
Chromosome Location	chr17:17600579-17600580
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17597833..17600762-chr17:17692593..17694977,2	MCF-7	breast:
2	chr17:17593686..17602682-chr17:17684488..17692992,14	MCF-7	breast:
3	chr17:17599477..17603323-chr17:17655564..17658131,3	MCF-7	breast:
4	chr17:17591306..17603641-chr17:17622226..17637880,43	MCF-7	breast:
5	chr17:17597990..17601613-chr17:17723911..17725744,3	MCF-7	breast:
6	chr17:17594258..17600676-chr17:17738917..17745175,15	MCF-7	breast:
7	chr17:17594932..17600890-chr17:17651321..17655426,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108557	Chromatin interaction
ENSG00000072310	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11656775	0.86[JPT][hapmap]
rs12940014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001884	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2350632	0.86[EUR][1000 genomes]
rs2350633	0.84[EUR][1000 genomes]
rs4496218	1.00[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs4925092	0.89[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4925093	0.89[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs4925094	0.89[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs4925096	0.82[EUR][1000 genomes]
rs4925102	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925104	1.00[CEU][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4925105	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4925109	0.86[JPT][hapmap]
rs6502613	0.92[CEU][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs6502615	0.89[CEU][hapmap]
rs7208561	0.85[CEU][hapmap]
rs7214245	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7224619	0.87[EUR][1000 genomes]
rs7224739	0.85[CEU][hapmap]
rs7225934	0.88[EUR][1000 genomes]
rs8065154	0.89[CEU][hapmap]
rs8075153	0.89[CEU][hapmap]
rs897457	0.88[EUR][1000 genomes]
rs941448	0.86[JPT][hapmap]
rs9897044	0.81[EUR][1000 genomes]
rs9897309	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9897596	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9900803	0.86[JPT][hapmap]
rs9904468	0.88[EUR][1000 genomes]
rs9906532	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv833384	chr17:17491483-17645648	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv907752	chr17:17569012-17750907	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
6	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
7	nsv907753	chr17:17573539-17747289	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
8	nsv907754	chr17:17573539-17782404	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS 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	78 gene(s)	inside rSNPs	diseases
9	nsv1061126	chr17:17578826-17803194	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv543238	chr17:17578826-17803194	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
11	nsv907755	chr17:17581184-17610587	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv833385	chr17:17594037-17765578	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
13	nsv1058884	chr17:17594370-17803194	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
14	nsv543240	chr17:17594370-17803194	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
15	nsv543241	chr17:17596222-17703059	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv1064176	chr17:17596222-17803194	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer 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 miRNA target site	77 gene(s)	inside rSNPs	diseases
17	nsv543242	chr17:17596222-17803194	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
18	nsv1062361	chr17:17598407-17746899	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
19	nsv543243	chr17:17598407-17746899	Genic enhancers Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7224617	TOM1L2	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17597400-17607000	Enhancers	Fetal Heart	heart
2	chr17:17598600-17607000	Enhancers	Fetal Lung	lung
3	chr17:17598800-17600800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr17:17598800-17600800	Enhancers	NHDF-Ad	bronchial
5	chr17:17598800-17601000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr17:17598800-17601200	Enhancers	Brain Substantia Nigra	brain
7	chr17:17598800-17601400	Enhancers	Fetal Intestine Small	intestine
8	chr17:17598800-17602200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr17:17598800-17602400	Enhancers	Gastric	stomach
10	chr17:17598800-17602800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:17598800-17603400	Enhancers	Spleen	Spleen
12	chr17:17598800-17603600	Enhancers	Esophagus	oesophagus
13	chr17:17598800-17603600	Enhancers	Right Atrium	heart
14	chr17:17598800-17604400	Enhancers	Fetal Muscle Trunk	muscle
15	chr17:17598800-17604800	Enhancers	Placenta Amnion	Placenta Amnion
16	chr17:17598800-17606800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr17:17598800-17608000	Enhancers	Lung	lung
18	chr17:17598800-17608000	Enhancers	Pancreas	Pancrea
19	chr17:17598800-17608200	Enhancers	Left Ventricle	heart
20	chr17:17599000-17600600	Enhancers	Brain Angular Gyrus	brain
21	chr17:17599000-17600800	Enhancers	HSMMtube	muscle
22	chr17:17599000-17601000	Enhancers	HSMM	muscle
23	chr17:17599000-17601400	Enhancers	Fetal Intestine Large	intestine
24	chr17:17599000-17602000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr17:17599000-17602200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr17:17599000-17602400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr17:17599000-17602600	Enhancers	Colon Smooth Muscle	Colon
28	chr17:17599000-17602800	Enhancers	Liver	Liver
29	chr17:17599000-17603200	Enhancers	Brain Anterior Caudate	brain
30	chr17:17599000-17603400	Enhancers	Brain Hippocampus Middle	brain
31	chr17:17599000-17603400	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr17:17599000-17603400	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr17:17599000-17603600	Enhancers	Brain Cingulate Gyrus	brain
34	chr17:17599000-17603600	Enhancers	Right Ventricle	heart
35	chr17:17599000-17603800	Enhancers	Adipose Nuclei	Adipose
36	chr17:17599000-17604400	Enhancers	Fetal Muscle Leg	muscle
37	chr17:17599000-17605800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr17:17599000-17606000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr17:17599200-17600800	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr17:17599200-17601200	Enhancers	Muscle Satellite Cultured Cells	--
41	chr17:17599200-17601400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr17:17599200-17601600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr17:17599200-17602200	Enhancers	Rectal Smooth Muscle	rectum
44	chr17:17599200-17602600	Enhancers	Psoas Muscle	Psoas
45	chr17:17599200-17602600	Enhancers	NHEK	skin
46	chr17:17599200-17602800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr17:17599200-17603000	Weak transcription	Small Intestine	intestine
48	chr17:17599200-17604000	Enhancers	Primary hematopoietic stem cells	blood
49	chr17:17599200-17607400	Enhancers	Stomach Mucosa	stomach
50	chr17:17599200-17615600	Weak transcription	Primary B cells from cord blood	blood

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