Variant report

Variant	rs3744493
Chromosome Location	chr17:66881125-66881126
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	chr17:66874045..66876700-chr17:66880164..66881823,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141338	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10852765	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11077801	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1156340	0.93[ASN][1000 genomes]
rs11651365	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12451990	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12452031	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12952511	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1373067	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1373068	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs16973376	0.85[AMR][1000 genomes]
rs34952002	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35241984	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3744492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744494	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3744495	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3744496	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4147313	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147314	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147993	0.82[CHD][hapmap];0.91[MEX][hapmap]
rs4147998	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4147999	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4148000	0.93[ASN][1000 genomes]
rs4148002	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4148004	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4148005	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4148008	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4148009	0.90[AMR][1000 genomes]
rs4148010	0.84[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes]
rs4968824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968825	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968968	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968970	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4968971	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4968972	0.86[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968973	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61303445	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66588031	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66600020	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67040494	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67927198	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68027451	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7503035	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8065105	0.93[ASN][1000 genomes]
rs8071218	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8074603	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8074769	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs991209	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs991210	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv908694	chr17:66802992-66913936	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv908695	chr17:66865583-66904001	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3744493	ICAM2	cis	cerebellum	SCAN
rs3744493	ACE	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66866800-66883600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr17:66869200-66903400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr17:66869800-66883400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr17:66875400-66881200	Strong transcription	Psoas Muscle	Psoas
5	chr17:66875600-66881400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr17:66876200-66882600	Weak transcription	Colon Smooth Muscle	Colon
7	chr17:66877000-66881200	Strong transcription	Brain Substantia Nigra	brain
8	chr17:66877000-66881400	Strong transcription	Fetal Muscle Trunk	muscle
9	chr17:66877000-66882400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr17:66877000-66883800	Strong transcription	Adipose Nuclei	Adipose
11	chr17:66877000-66884000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr17:66877000-66886200	Weak transcription	Colonic Mucosa	Colon
13	chr17:66877000-66886600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr17:66877000-66889000	Weak transcription	Spleen	Spleen
15	chr17:66877000-66906200	Weak transcription	Fetal Stomach	stomach
16	chr17:66877200-66882000	Strong transcription	Left Ventricle	heart
17	chr17:66877200-66882400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr17:66877200-66882800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr17:66877200-66887400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr17:66877400-66882600	Weak transcription	Placenta	Placenta
21	chr17:66877600-66888400	Strong transcription	Liver	Liver
22	chr17:66877600-66893400	Weak transcription	Brain Anterior Caudate	brain
23	chr17:66877800-66918200	Weak transcription	Fetal Brain Male	brain
24	chr17:66878200-66881800	Strong transcription	Ovary	ovary
25	chr17:66878200-66889400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr17:66878200-66899200	Weak transcription	Osteobl	bone
27	chr17:66878400-66901000	Weak transcription	Brain Angular Gyrus	brain
28	chr17:66879600-66881400	Strong transcription	Fetal Heart	heart
29	chr17:66879800-66892600	Weak transcription	Fetal Muscle Leg	muscle
30	chr17:66879800-66897000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr17:66880000-66893400	Weak transcription	Brain Hippocampus Middle	brain
32	chr17:66880600-66881200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr17:66880600-66881400	Strong transcription	Brain Cingulate Gyrus	brain
34	chr17:66880600-66881400	Strong transcription	Right Ventricle	heart
35	chr17:66880600-66881400	Enhancers	HepG2	liver
36	chr17:66880800-66881200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr17:66880800-66881400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:66880800-66881600	Genic enhancers	Fetal Lung	lung
39	chr17:66880800-66883800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr17:66881000-66882400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr17:66881000-66903200	Weak transcription	Brain Inferior Temporal Lobe	brain

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