Variant report

Variant	rs17207481
Chromosome Location	chr19:57006415-57006416
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:57002795..57005630-chr19:57006374..57008169,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC004696.1-1	chr19:57005532-57006805	NONHSAT068156
2	lnc-AC004696.1-1	chr19:57005532-57006801	ENSG00000166770.6
3	lnc-AC004696.1-1	chr19:57005532-57006805	NONHSAT068157

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12709959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs12979827	0.89[AMR][1000 genomes]
rs16987342	1.00[YRI][hapmap]
rs17207432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215410	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2288862	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2288863	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs28815239	0.86[AMR][1000 genomes]
rs34403290	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35215648	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35520457	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36147582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801316	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4801318	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4801720	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs62121592	0.88[AMR][1000 genomes]
rs62121594	0.88[AMR][1000 genomes]
rs62121597	0.89[AMR][1000 genomes]
rs8113270	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9646635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749115	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv912518	chr19:56995737-57109821	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17207481	MGC9913	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56990800-57010000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:56991200-57006800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr19:56991200-57006800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:56992000-57009400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
5	chr19:56992000-57009800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr19:56998600-57008800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
7	chr19:57002800-57006800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr19:57003000-57018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:57003200-57018400	Weak transcription	Osteobl	bone
10	chr19:57003600-57006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:57003600-57017000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:57003800-57006800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:57003800-57011600	Weak transcription	Fetal Heart	heart
14	chr19:57004400-57006800	Weak transcription	Fetal Brain Male	brain
15	chr19:57004400-57008800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr19:57004600-57009400	ZNF genes & repeats	Ovary	ovary
17	chr19:57004600-57009600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:57004800-57007800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr19:57004800-57007800	Strong transcription	Right Ventricle	heart
20	chr19:57005000-57006600	Weak transcription	Colon Smooth Muscle	Colon
21	chr19:57005000-57006800	Weak transcription	Fetal Intestine Large	intestine
22	chr19:57005000-57007000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:57005200-57006600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:57005200-57008000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:57005400-57006600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:57005400-57006800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:57005400-57006800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:57005400-57007200	Strong transcription	Fetal Muscle Leg	muscle
29	chr19:57005400-57007600	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr19:57005400-57007800	ZNF genes & repeats	Adipose Nuclei	Adipose
31	chr19:57005400-57007800	Strong transcription	Left Ventricle	heart
32	chr19:57005400-57008400	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr19:57005400-57008400	ZNF genes & repeats	Spleen	Spleen
34	chr19:57005400-57008600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr19:57005400-57009000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:57005400-57009200	ZNF genes & repeats	Aorta	Aorta
37	chr19:57005400-57010000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:57005600-57006800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:57005600-57006800	Strong transcription	Brain Hippocampus Middle	brain
40	chr19:57005600-57007000	Weak transcription	Pancreas	Pancrea
41	chr19:57005600-57007000	Strong transcription	HSMM	muscle
42	chr19:57005600-57007200	Strong transcription	HSMMtube	muscle
43	chr19:57005600-57007400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr19:57005600-57008000	ZNF genes & repeats	Fetal Lung	lung
45	chr19:57005600-57009600	Strong transcription	Brain Anterior Caudate	brain
46	chr19:57005800-57006600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:57005800-57006600	Weak transcription	Brain Angular Gyrus	brain
48	chr19:57005800-57006600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr19:57005800-57006600	Weak transcription	Fetal Brain Female	brain
50	chr19:57005800-57006800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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