Variant report

Variant	rs7208561
Chromosome Location	chr17:17615528-17615529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17615254..17617697-chr17:17640726..17643418,2	MCF-7	breast:
2	chr17:17257197..17259273-chr17:17614438..17616951,2	K562	blood:
3	chr17:17612996..17615651-chr17:17616150..17617784,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12940014	0.85[CEU][hapmap]
rs12942059	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12945601	0.92[JPT][hapmap]
rs2001884	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4496218	0.85[CEU][hapmap]
rs4925092	0.82[CEU][hapmap]
rs4925093	0.82[CEU][hapmap]
rs4925094	0.82[CEU][hapmap]
rs4925104	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs4925105	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs4925108	0.92[JPT][hapmap]
rs6502613	0.93[CEU][hapmap];0.80[TSI][hapmap]
rs6502615	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224617	0.85[CEU][hapmap]
rs7224739	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8065154	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8075153	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs941444	0.92[JPT][hapmap]
rs9897309	0.85[CEU][hapmap];0.90[CHD][hapmap];0.80[MEX][hapmap]
rs9899445	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9910411	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7208561	TOM1L2	cis	parietal	SCAN
rs7208561	CDRT4	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17599200-17615600	Weak transcription	Primary B cells from cord blood	blood
2	chr17:17599400-17617200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr17:17599400-17617400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr17:17601400-17617600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr17:17606400-17615600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr17:17608600-17620400	Weak transcription	Dnd41	blood
7	chr17:17608800-17615600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr17:17609200-17616600	Enhancers	Fetal Intestine Large	intestine
9	chr17:17609400-17618200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr17:17610000-17615600	Weak transcription	Liver	Liver
11	chr17:17611000-17616000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr17:17611400-17616000	Enhancers	Fetal Lung	lung
13	chr17:17611400-17617600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr17:17612200-17616200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr17:17612200-17617000	Weak transcription	Adipose Nuclei	Adipose
16	chr17:17612400-17615800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:17612600-17616000	Enhancers	Lung	lung
18	chr17:17612600-17616200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:17612600-17616200	Enhancers	Placenta Amnion	Placenta Amnion
20	chr17:17612600-17616400	Enhancers	Stomach Mucosa	stomach
21	chr17:17612800-17616000	Enhancers	Pancreas	Pancrea
22	chr17:17612800-17618000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr17:17613000-17618400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr17:17613200-17616000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
25	chr17:17613200-17616000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:17613200-17616000	Enhancers	Right Ventricle	heart
27	chr17:17613200-17616200	Enhancers	Brain Anterior Caudate	brain
28	chr17:17613200-17616200	Enhancers	Left Ventricle	heart
29	chr17:17613200-17618000	Enhancers	HMEC	breast
30	chr17:17613200-17620200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr17:17613400-17615600	Enhancers	HUVEC	blood vessel
32	chr17:17613400-17617000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr17:17613400-17617200	Enhancers	Colon Smooth Muscle	Colon
34	chr17:17613400-17618200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr17:17613400-17621600	Weak transcription	Thymus	Thymus
36	chr17:17613600-17615600	Enhancers	Brain Angular Gyrus	brain
37	chr17:17613600-17616000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr17:17613600-17616000	Enhancers	Esophagus	oesophagus
39	chr17:17613600-17616200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:17613600-17616200	Enhancers	NHEK	skin
41	chr17:17613600-17616400	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr17:17613600-17617000	Weak transcription	Primary T cells from cord blood	blood
43	chr17:17613600-17617200	Enhancers	Muscle Satellite Cultured Cells	--
44	chr17:17613600-17617600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr17:17613600-17617600	Enhancers	NHDF-Ad	bronchial
46	chr17:17613600-17618600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr17:17613600-17624400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr17:17613800-17615800	Enhancers	Fetal Muscle Leg	muscle
49	chr17:17613800-17616000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr17:17613800-17616000	Enhancers	Fetal Muscle Trunk	muscle

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