Variant report

Variant	rs36053156
Chromosome Location	chr6:86575509-86575510
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86386983..86389313-chr6:86573645..86576019,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10806337	0.81[ASN][1000 genomes]
rs10944137	0.82[ASN][1000 genomes]
rs10944138	0.85[ASN][1000 genomes]
rs10944144	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10944145	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10944147	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10944151	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10944152	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10944157	0.91[EUR][1000 genomes]
rs11752180	0.99[EUR][1000 genomes]
rs11752223	0.99[EUR][1000 genomes]
rs11754330	0.82[ASN][1000 genomes]
rs11755642	0.82[ASN][1000 genomes]
rs11758508	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12153887	0.91[EUR][1000 genomes]
rs12191212	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12192546	0.82[ASN][1000 genomes]
rs12193904	0.82[ASN][1000 genomes]
rs12196377	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12198061	0.92[EUR][1000 genomes]
rs12198557	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12198730	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12199329	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12201741	0.82[EUR][1000 genomes]
rs12202712	0.97[EUR][1000 genomes]
rs12205492	0.82[ASN][1000 genomes]
rs12209668	0.95[EUR][1000 genomes]
rs12211216	0.90[EUR][1000 genomes]
rs12215159	0.81[EUR][1000 genomes]
rs12660846	0.99[EUR][1000 genomes]
rs12665464	0.99[EUR][1000 genomes]
rs12665516	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12665542	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13201730	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13203309	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13203560	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13207537	0.92[EUR][1000 genomes]
rs13209671	0.93[EUR][1000 genomes]
rs13209740	0.85[EUR][1000 genomes]
rs13213603	0.89[EUR][1000 genomes]
rs13219504	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1335442	0.80[ASN][1000 genomes]
rs1447160	0.90[EUR][1000 genomes]
rs1470531	0.81[EUR][1000 genomes]
rs1813001	0.91[EUR][1000 genomes]
rs1838954	0.95[EUR][1000 genomes]
rs1838955	0.95[EUR][1000 genomes]
rs1838958	0.94[EUR][1000 genomes]
rs1838959	0.92[EUR][1000 genomes]
rs2084293	0.95[EUR][1000 genomes]
rs2084294	0.95[EUR][1000 genomes]
rs2084296	0.91[EUR][1000 genomes]
rs2084297	0.90[EUR][1000 genomes]
rs2100109	0.91[EUR][1000 genomes]
rs2121594	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166665	0.91[EUR][1000 genomes]
rs2197648	0.91[EUR][1000 genomes]
rs2218594	0.91[EUR][1000 genomes]
rs2225754	0.82[ASN][1000 genomes]
rs2875456	0.82[EUR][1000 genomes]
rs34622605	0.81[ASN][1000 genomes]
rs34765423	0.85[ASN][1000 genomes]
rs35874630	0.86[EUR][1000 genomes]
rs36035797	0.91[EUR][1000 genomes]
rs4706246	0.86[EUR][1000 genomes]
rs4706248	0.90[EUR][1000 genomes]
rs4706252	0.92[EUR][1000 genomes]
rs4706253	0.92[EUR][1000 genomes]
rs4706254	0.81[EUR][1000 genomes]
rs4707223	0.83[EUR][1000 genomes]
rs4707229	0.91[EUR][1000 genomes]
rs4707236	0.82[EUR][1000 genomes]
rs57016132	0.92[EUR][1000 genomes]
rs61119084	0.87[EUR][1000 genomes]
rs67024565	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6900436	0.82[EUR][1000 genomes]
rs72907388	0.81[ASN][1000 genomes]
rs7739241	0.97[EUR][1000 genomes]
rs7755730	0.99[EUR][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	nsv1028293	chr6:86353958-86778912	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases
2	nsv538350	chr6:86353958-86778912	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases
3	nsv886335	chr6:86445651-86669361	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1022618	chr6:86465365-87432069	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv538352	chr6:86465365-87432069	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1033637	chr6:86482045-86701733	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538353	chr6:86482045-86701733	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv526067	chr6:86538718-86576854	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1802672	chr6:86546123-86662267	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv522858	chr6:86550985-86578833	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1018453	chr6:86555984-86761120	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv3451810	chr6:86564474-86577360	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs36053156	SNHG5	cis	Thyroid	GTEx
rs36053156	SNHG5	cis	Esophagus Muscularis	GTEx
rs36053156	SNHG5	cis	Nerve Tibial	GTEx
rs36053156	SNHG5	cis	Artery Tibial	GTEx
rs36053156	SNHG5	cis	lung	GTEx
rs36053156	SNHG5	cis	Muscle Skeletal	GTEx
rs36053156	SNHG5	cis	Heart Left Ventricle	GTEx
rs36053156	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs36053156	SNHG5	cis	Adipose Subcutaneous	GTEx
rs36053156	SNHG5	cis	multi-tissue	Pritchard
rs36053156	SNHG5	cis	Esophagus Mucosa	GTEx
rs36053156	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs36053156	SNHG5	cis	Whole Blood	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86563200-86577800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:86568200-86576800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:86573400-86575600	Enhancers	Pancreas	Pancrea
4	chr6:86574400-86575600	Enhancers	Esophagus	oesophagus
5	chr6:86574400-86575600	Enhancers	Small Intestine	intestine
6	chr6:86574400-86576400	Active TSS	NHDF-Ad	bronchial
7	chr6:86574600-86575600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:86574600-86576000	Enhancers	Fetal Heart	heart
9	chr6:86574600-86576200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr6:86574600-86576200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:86574600-86576200	Active TSS	Brain Angular Gyrus	brain
12	chr6:86574600-86576600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr6:86574800-86575600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:86574800-86575600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:86574800-86575600	Enhancers	Fetal Brain Female	brain
16	chr6:86574800-86575600	Flanking Active TSS	Ovary	ovary
17	chr6:86574800-86575800	Enhancers	Fetal Brain Male	brain
18	chr6:86574800-86576200	Active TSS	Aorta	Aorta
19	chr6:86574800-86576200	Flanking Active TSS	HUVEC	blood vessel
20	chr6:86575000-86575600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:86575000-86575600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:86575000-86575600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:86575000-86575600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:86575000-86575600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:86575000-86575600	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr6:86575000-86575600	Flanking Active TSS	HMEC	breast
27	chr6:86575000-86575800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:86575000-86575800	Enhancers	Spleen	Spleen
29	chr6:86575000-86576200	Flanking Active TSS	Dnd41	blood
30	chr6:86575000-86576400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:86575000-86576400	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr6:86575000-86576600	Active TSS	Colonic Mucosa	Colon
33	chr6:86575000-86576600	Enhancers	Lung	lung
34	chr6:86575000-86576600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr6:86575000-86577000	Enhancers	H1 Cell Line	embryonic stem cell
36	chr6:86575200-86575600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:86575200-86575600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:86575200-86575600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:86575200-86575600	Flanking Active TSS	Fetal Kidney	kidney
40	chr6:86575200-86575600	Flanking Active TSS	Fetal Lung	lung
41	chr6:86575200-86575600	Enhancers	Psoas Muscle	Psoas
42	chr6:86575200-86575600	Flanking Active TSS	Osteobl	bone
43	chr6:86575200-86575800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:86575200-86575800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr6:86575200-86576000	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr6:86575200-86576000	Active TSS	Primary hematopoietic stem cells	blood
47	chr6:86575200-86576000	Active TSS	Monocytes-CD14+_RO01746	blood
48	chr6:86575200-86576200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:86575200-86576200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:86575200-86576200	Active TSS	Rectal Smooth Muscle	rectum

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