Variant report

Variant	rs17828568
Chromosome Location	chr6:1574101-1574102
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GMDS-6	chr6:1573891-1574384	NONHSAT106519
2	lnc-GMDS-6	chr6:1573891-1574384	NONHSAT106520

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11967512	1.00[CHD][hapmap]
rs12523787	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525317	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12530463	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191308	1.00[ASN][1000 genomes]
rs13197210	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201037	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13209162	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210401	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13212794	1.00[ASN][1000 genomes]
rs13214070	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2015974	1.00[ASN][1000 genomes]
rs2317967	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317968	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745610	1.00[ASN][1000 genomes]
rs2816224	1.00[ASN][1000 genomes]
rs2816225	1.00[ASN][1000 genomes]
rs34114087	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34779492	1.00[ASN][1000 genomes]
rs35040319	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35412353	1.00[ASN][1000 genomes]
rs35694654	1.00[ASN][1000 genomes]
rs35793648	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361530	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4367416	1.00[ASN][1000 genomes]
rs55821127	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62388633	1.00[ASN][1000 genomes]
rs62388638	1.00[ASN][1000 genomes]
rs62388641	1.00[ASN][1000 genomes]
rs62390562	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6596831	1.00[ASN][1000 genomes]
rs71550060	1.00[ASN][1000 genomes]
rs910016	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024111	chr6:1231850-1730146	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1021924	chr6:1254891-1736995	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv538082	chr6:1254891-1736995	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv917248	chr6:1365437-1627813	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1034039	chr6:1427061-1691837	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv538088	chr6:1427061-1691837	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
8	nsv1027393	chr6:1446300-1692019	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv538089	chr6:1446300-1692019	Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv1016859	chr6:1460020-1645819	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv883376	chr6:1535043-1635082	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv883377	chr6:1552705-1583600	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17828568	RP11-157J24.2	cis	Esophagus Muscularis	GTEx
rs17828568	RP11-157J24.2	cis	Muscle Skeletal	GTEx
rs17828568	RP11-157J24.2	cis	lung	GTEx
rs17828568	TUBB2A	cis	cerebellum	SCAN
rs17828568	RP11-157J24.2	cis	Esophagus Mucosa	GTEx
rs17828568	RP11-157J24.2	cis	Thyroid	GTEx
rs17828568	RP11-157J24.2	cis	Artery Tibial	GTEx
rs17828568	RP11-157J24.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1572800-1575600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:1573200-1575200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:1573200-1575600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:1573200-1576200	Enhancers	Esophagus	oesophagus
5	chr6:1573400-1575400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:1573400-1576600	Enhancers	GM12878-XiMat	blood
7	chr6:1573600-1575000	Weak transcription	HSMMtube	muscle
8	chr6:1573600-1576000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:1573600-1576200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr6:1573800-1574200	Enhancers	Brain Hippocampus Middle	brain
11	chr6:1573800-1575200	Weak transcription	HSMM	muscle
12	chr6:1573800-1575400	Enhancers	Stomach Smooth Muscle	stomach
13	chr6:1574000-1574800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:1574000-1575400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:1574000-1575800	Enhancers	Fetal Stomach	stomach
16	chr6:1574000-1576000	Enhancers	Fetal Thymus	thymus
17	chr6:1574000-1576200	Enhancers	Brain Anterior Caudate	brain
18	chr6:1574000-1576600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr6:1574000-1576800	Enhancers	Brain Angular Gyrus	brain
20	chr6:1574000-1577000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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