Variant report

Variant	rs17040519
Chromosome Location	chr4:110466758-110466759
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110463063..110464866-chr4:110466518..110468456,2	MCF-7	breast:
2	chr4:110466638..110469623-chr4:110471525..110474014,2	K562	blood:
3	chr4:110461566..110463825-chr4:110465703..110468687,3	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10488879	0.81[ASN][1000 genomes]
rs10488910	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs10516557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11098033	0.81[ASW][hapmap];1.00[CEU][hapmap]
rs11098035	1.00[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11934486	0.93[EUR][1000 genomes]
rs11935629	1.00[CEU][hapmap]
rs11937053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11941636	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11943384	1.00[CEU][hapmap]
rs11943430	1.00[CEU][hapmap]
rs11944659	0.86[EUR][1000 genomes]
rs12639835	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12640161	0.93[EUR][1000 genomes]
rs12641472	0.92[ASN][1000 genomes]
rs12642304	0.90[EUR][1000 genomes]
rs12643844	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12643881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648138	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12650654	0.81[ASW][hapmap];1.00[CEU][hapmap]
rs13128221	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17040446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17040454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17040512	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17585970	0.85[TSI][hapmap]
rs17619262	0.85[TSI][hapmap]
rs17619310	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs28527792	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28611124	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61242473	0.85[EUR][1000 genomes]
rs6815455	1.00[CEU][hapmap]
rs6821051	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821221	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823032	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6825928	0.84[CHD][hapmap]
rs72896619	0.93[EUR][1000 genomes]
rs72896622	0.93[EUR][1000 genomes]
rs72896625	0.93[EUR][1000 genomes]
rs72896629	0.93[EUR][1000 genomes]
rs7436745	0.81[ASW][hapmap];1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110393800-110469200	Weak transcription	Stomach Mucosa	stomach
2	chr4:110409400-110467800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr4:110412400-110470600	Strong transcription	Fetal Thymus	thymus
4	chr4:110423400-110480800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:110424800-110468400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:110425200-110468000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:110434800-110469600	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr4:110435000-110468400	Strong transcription	Liver	Liver
9	chr4:110436800-110468000	Strong transcription	HSMM	muscle
10	chr4:110445800-110467800	Strong transcription	Adipose Nuclei	Adipose
11	chr4:110448800-110479600	Weak transcription	Small Intestine	intestine
12	chr4:110448800-110480000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:110449600-110469400	Weak transcription	Pancreas	Pancrea
14	chr4:110452000-110467000	Weak transcription	Spleen	Spleen
15	chr4:110452000-110470200	Weak transcription	Esophagus	oesophagus
16	chr4:110452400-110480800	Weak transcription	Right Ventricle	heart
17	chr4:110454000-110480600	Weak transcription	NHLF	lung
18	chr4:110454600-110480200	Weak transcription	A549	lung
19	chr4:110455000-110470800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr4:110455400-110469400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:110455400-110469800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:110455600-110480600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:110456200-110467200	Weak transcription	Aorta	Aorta
24	chr4:110456200-110470800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr4:110456400-110469000	Weak transcription	HMEC	breast
26	chr4:110456400-110469400	Weak transcription	Brain Angular Gyrus	brain
27	chr4:110456400-110472000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr4:110456400-110480600	Weak transcription	Brain Substantia Nigra	brain
29	chr4:110456400-110481600	Weak transcription	Fetal Heart	heart
30	chr4:110456600-110469600	Weak transcription	Lung	lung
31	chr4:110457400-110467200	Weak transcription	Brain Germinal Matrix	brain
32	chr4:110457400-110468400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:110457400-110480600	Weak transcription	Right Atrium	heart
34	chr4:110458400-110466800	Strong transcription	NH-A	brain
35	chr4:110458400-110469000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:110458800-110469600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:110459000-110467400	Strong transcription	Placenta	Placenta
38	chr4:110460200-110480800	Weak transcription	Brain Anterior Caudate	brain
39	chr4:110461000-110467600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr4:110461000-110468600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:110461000-110480600	Weak transcription	HSMMtube	muscle
42	chr4:110461200-110467400	Weak transcription	Ovary	ovary
43	chr4:110461200-110471000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr4:110461200-110479600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:110461600-110470400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr4:110462000-110469400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr4:110462000-110469400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr4:110462000-110478400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr4:110462400-110474400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr4:110462600-110469600	Weak transcription	Placenta Amnion	Placenta Amnion

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