Variant report

Variant	rs13212794
Chromosome Location	chr6:1548584-1548585
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	chr6:1538946..1541527-chr6:1548502..1550339,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GMDS-6	chr6:1548086-1553288	NONHSAT106513
2	lnc-GMDS-6	chr6:1548086-1553288	NONHSAT106514

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12523787	1.00[ASN][1000 genomes]
rs12525317	1.00[ASN][1000 genomes]
rs12530463	1.00[ASN][1000 genomes]
rs13191308	1.00[ASN][1000 genomes]
rs13197210	1.00[ASN][1000 genomes]
rs13201037	1.00[ASN][1000 genomes]
rs13203964	1.00[ASN][1000 genomes]
rs13209162	1.00[ASN][1000 genomes]
rs13210401	1.00[ASN][1000 genomes]
rs17828568	1.00[ASN][1000 genomes]
rs2015974	1.00[ASN][1000 genomes]
rs2317967	1.00[ASN][1000 genomes]
rs2317968	1.00[ASN][1000 genomes]
rs2745610	1.00[ASN][1000 genomes]
rs2816224	1.00[ASN][1000 genomes]
rs2816225	1.00[ASN][1000 genomes]
rs34114087	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34779492	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35040319	1.00[ASN][1000 genomes]
rs35412353	1.00[ASN][1000 genomes]
rs35694654	1.00[ASN][1000 genomes]
rs35793648	1.00[ASN][1000 genomes]
rs361530	1.00[ASN][1000 genomes]
rs4367416	1.00[ASN][1000 genomes]
rs55821127	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][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	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][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:13 , 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	nsv883374	chr6:1454334-1558449	Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	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
12	nsv883375	chr6:1478613-1558449	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs13212794	RP11-157J24.2	cis	lung	GTEx
rs13212794	RP11-157J24.2	cis	Thyroid	GTEx
rs13212794	RP11-157J24.2	cis	Muscle Skeletal	GTEx
rs13212794	RP11-157J24.2	cis	Esophagus Mucosa	GTEx
rs13212794	RP11-157J24.2	cis	Skin Sun Exposed Lower leg	GTEx
rs13212794	RP11-157J24.2	cis	Nerve Tibial	GTEx
rs13212794	RP11-157J24.2	cis	Esophagus Muscularis	GTEx
rs13212794	RP11-157J24.2	cis	Artery Tibial	GTEx
rs13212794	RP11-157J24.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1527800-1555000	Weak transcription	Gastric	stomach
2	chr6:1535800-1554400	Weak transcription	Psoas Muscle	Psoas
3	chr6:1536000-1554000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr6:1537200-1554000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:1537600-1553200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:1538000-1552600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:1538000-1554400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:1538200-1552600	Weak transcription	Brain Anterior Caudate	brain
9	chr6:1538600-1554000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:1538600-1554200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:1538800-1552600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:1539200-1549600	Weak transcription	Brain Angular Gyrus	brain
13	chr6:1539400-1554400	Weak transcription	Right Ventricle	heart
14	chr6:1539600-1554000	Weak transcription	NHDF-Ad	bronchial
15	chr6:1541800-1551800	Weak transcription	Liver	Liver
16	chr6:1543000-1549200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:1543200-1552200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:1543800-1554200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:1544200-1548800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:1544200-1554000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:1544400-1554000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr6:1545000-1549400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:1545800-1548800	Strong transcription	Aorta	Aorta
24	chr6:1545800-1554200	Weak transcription	HSMM	muscle
25	chr6:1546000-1549000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:1546400-1548800	Strong transcription	Ovary	ovary
27	chr6:1546400-1549000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:1546400-1549000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr6:1546400-1554200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:1546600-1554400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:1547000-1554400	Weak transcription	A549	lung
32	chr6:1547400-1554600	Weak transcription	Brain Substantia Nigra	brain
33	chr6:1547800-1548600	Strong transcription	Osteobl	bone
34	chr6:1547800-1548800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:1547800-1549000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:1547800-1549000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:1547800-1549000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:1547800-1549000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:1547800-1549200	Strong transcription	Adipose Nuclei	Adipose
40	chr6:1548000-1549000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr6:1548200-1550000	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:1548200-1554400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:1548200-1554400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr6:1548200-1554600	Weak transcription	Fetal Stomach	stomach
45	chr6:1548200-1554800	Weak transcription	Esophagus	oesophagus
46	chr6:1548400-1554400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:1548400-1554600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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