Variant report

Variant	rs1056682
Chromosome Location	chr15:50660201-50660202
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	chr15:50658523..50661516-chr15:50743007..50745833,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP8-2	chr15:50659606-50660286	NONHSAT042412
2	lnc-USP8-2	chr15:50659561-50660476	ENSG00000246338

Extended variants
information (count: 28 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11634585	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12905221	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12911017	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17431095	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17431150	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17431171	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1806843	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2555486	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28489579	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28817272	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34174311	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34565064	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35541701	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35628775	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35831049	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4775880	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55941574	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55948407	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs606118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66904653	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7164848	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7182201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs720599	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats 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 miRNA target site	119 gene(s)	inside rSNPs	diseases
5	nsv524613	chr15:50656449-50868779	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1056682	CTD-3110H11.1	cis	lung	GTEx
rs1056682	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs1056682	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs1056682	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs1056682	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs1056682	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs1056682	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs1056682	GABPB2	cis	uninvolved skin	skin_eQTL
rs1056682	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs1056682	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs1056682	GABPB1-AS1	cis	Nerve Tibial	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50648000-50667600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:50648200-50664400	Weak transcription	Lung	lung
3	chr15:50648400-50660400	Weak transcription	Aorta	Aorta
4	chr15:50649200-50664400	Weak transcription	Right Ventricle	heart
5	chr15:50649400-50664000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:50649600-50660600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:50649600-50661800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:50649800-50664200	Weak transcription	Small Intestine	intestine
9	chr15:50649800-50664600	Weak transcription	Psoas Muscle	Psoas
10	chr15:50650000-50663000	Weak transcription	Fetal Brain Male	brain
11	chr15:50650000-50663600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:50650200-50662600	Weak transcription	NH-A	brain
13	chr15:50650200-50664000	Weak transcription	Spleen	Spleen
14	chr15:50651400-50660600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr15:50651400-50660800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:50651400-50661600	Weak transcription	NHDF-Ad	bronchial
17	chr15:50651400-50664600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:50653000-50662600	Weak transcription	Brain Angular Gyrus	brain
19	chr15:50653000-50664600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:50653200-50662800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:50653200-50666800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr15:50653400-50662600	Weak transcription	Fetal Intestine Small	intestine
23	chr15:50654200-50664400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:50654200-50665000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:50654400-50662800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:50654400-50662800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:50654400-50666400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr15:50654400-50670600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:50654600-50661400	Weak transcription	Fetal Kidney	kidney
30	chr15:50654600-50663000	Weak transcription	Brain Anterior Caudate	brain
31	chr15:50654600-50664000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr15:50654600-50664400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:50654600-50664400	Weak transcription	Fetal Lung	lung
34	chr15:50654600-50664400	Weak transcription	Osteobl	bone
35	chr15:50654600-50664600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:50654600-50666000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr15:50654800-50662800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr15:50655000-50661400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr15:50655000-50662200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr15:50655200-50663600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr15:50655200-50664400	Weak transcription	HMEC	breast
42	chr15:50655400-50662800	Weak transcription	NHLF	lung
43	chr15:50655400-50664600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:50655600-50662200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr15:50655600-50664600	Weak transcription	Fetal Intestine Large	intestine
46	chr15:50655600-50665200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:50655600-50665400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:50655800-50664200	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:50655800-50666000	Weak transcription	Brain Germinal Matrix	brain
50	chr15:50655800-50666000	Weak transcription	Left Ventricle	heart

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