Variant report

Variant	rs2745610
Chromosome Location	chr6:1553976-1553977
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1540042..1541785-chr6:1551983..1554224,2	MCF-7	breast:
2	chr6:1500696..1503622-chr6:1553281..1556067,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GMDS-6	chr6:1548843-1554045	NONHSAT106515
2	lnc-GMDS-6	chr6:1548843-1554045	NONHSAT106516

Extended variants
information (count: 47 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:33)

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]
rs13212794	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]
rs2816224	1.00[ASN][1000 genomes]
rs2816225	1.00[ASN][1000 genomes]
rs34114087	1.00[ASN][1000 genomes]
rs34779492	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[ASN][1000 genomes]
rs62388633	1.00[ASN][1000 genomes]
rs62388638	1.00[ASN][1000 genomes]
rs62388641	1.00[ASN][1000 genomes]
rs62390562	1.00[ASN][1000 genomes]
rs6596831	1.00[ASN][1000 genomes]
rs71550060	1.00[ASN][1000 genomes]
rs910016	1.00[ASN][1000 genomes]
rs9391923	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
14	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2745610	RP11-157J24.2	cis	Thyroid	GTEx
rs2745610	RP11-157J24.2	cis	lung	GTEx
rs2745610	RP11-157J24.2	cis	Muscle Skeletal	GTEx
rs2745610	RP11-157J24.2	cis	Nerve Tibial	GTEx
rs2745610	RP11-157J24.2	cis	Esophagus Mucosa	GTEx
rs2745610	RP11-157J24.2	cis	Adipose Subcutaneous	GTEx
rs2745610	TUBB2A	cis	cerebellum	SCAN
rs2745610	RP11-157J24.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2745610	RP11-157J24.2	cis	Artery Tibial	GTEx
rs2745610	RP11-157J24.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

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	chr6:1538000-1554400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:1538600-1554000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:1538600-1554200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:1539400-1554400	Weak transcription	Right Ventricle	heart
9	chr6:1539600-1554000	Weak transcription	NHDF-Ad	bronchial
10	chr6:1543800-1554200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:1544200-1554000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:1544400-1554000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr6:1545800-1554200	Weak transcription	HSMM	muscle
14	chr6:1546400-1554200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:1546600-1554400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:1547000-1554400	Weak transcription	A549	lung
17	chr6:1547400-1554600	Weak transcription	Brain Substantia Nigra	brain
18	chr6:1548200-1554400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:1548200-1554400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:1548200-1554600	Weak transcription	Fetal Stomach	stomach
21	chr6:1548200-1554800	Weak transcription	Esophagus	oesophagus
22	chr6:1548400-1554400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:1548400-1554600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:1548600-1554000	Weak transcription	Osteobl	bone
25	chr6:1548800-1554400	Weak transcription	Aorta	Aorta
26	chr6:1548800-1554800	Weak transcription	Ovary	ovary
27	chr6:1549000-1554000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:1549000-1554000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:1549000-1554000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:1549000-1554400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr6:1549000-1555000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:1552600-1554000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:1552600-1554000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:1552600-1554600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:1552600-1555000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:1552800-1554200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:1552800-1554400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:1553000-1554000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:1553000-1554600	Weak transcription	Brain Anterior Caudate	brain
40	chr6:1553000-1554600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:1553200-1554200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:1553200-1554200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr6:1553200-1554600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:1553400-1554200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr6:1553400-1554600	Weak transcription	Liver	Liver
46	chr6:1553400-1554800	Weak transcription	HMEC	breast
47	chr6:1553400-1555000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:1553600-1554000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:1553600-1554000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:1553600-1554000	Weak transcription	Adipose Nuclei	Adipose

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