Variant report

Variant	rs57016132
Chromosome Location	chr6:86552556-86552557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10944136	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10944138	0.81[EUR][1000 genomes]
rs10944144	0.94[EUR][1000 genomes]
rs10944145	0.94[EUR][1000 genomes]
rs10944147	0.98[EUR][1000 genomes]
rs10944151	0.96[EUR][1000 genomes]
rs10944152	0.97[EUR][1000 genomes]
rs10944157	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11752180	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11752223	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11758508	0.85[EUR][1000 genomes]
rs12153887	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12190603	0.80[ASN][1000 genomes]
rs12191212	0.97[EUR][1000 genomes]
rs12196377	0.96[EUR][1000 genomes]
rs12198061	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12198557	0.89[EUR][1000 genomes]
rs12198730	0.97[EUR][1000 genomes]
rs12199329	0.94[EUR][1000 genomes]
rs12202712	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12209668	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211216	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12215159	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12660846	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12665464	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12665516	0.94[EUR][1000 genomes]
rs12665542	0.94[EUR][1000 genomes]
rs13192974	0.84[AMR][1000 genomes]
rs13201730	0.98[EUR][1000 genomes]
rs13203309	0.94[EUR][1000 genomes]
rs13203560	0.95[EUR][1000 genomes]
rs13207173	0.83[AMR][1000 genomes]
rs13207537	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13209671	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13209740	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13213603	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13214489	0.92[AMR][1000 genomes]
rs13219504	0.98[EUR][1000 genomes]
rs1447160	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1470531	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1813001	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1838954	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1838955	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1838958	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1838959	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2084293	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2084294	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2084296	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2084297	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2100109	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2121594	0.90[EUR][1000 genomes]
rs2166665	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2197648	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2218594	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2324817	0.80[AMR][1000 genomes]
rs34765423	0.81[EUR][1000 genomes]
rs34795473	0.83[AMR][1000 genomes]
rs35874630	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36035797	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36053156	0.92[EUR][1000 genomes]
rs4098044	0.83[AMR][1000 genomes]
rs4706246	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4706247	0.86[AMR][1000 genomes]
rs4706248	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4706252	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4706253	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4707223	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4707229	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61119084	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6454487	0.80[AMR][1000 genomes]
rs6454488	0.80[AMR][1000 genomes]
rs66807489	0.83[AMR][1000 genomes]
rs67024565	0.98[EUR][1000 genomes]
rs6900436	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7739241	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7755730	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9647601	0.81[AMR][1000 genomes];0.80[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	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	nsv1034677	chr6:86474368-86566463	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv515896	chr6:86538718-86573165	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh	lncRNA	n/a	inside rSNPs	diseases
10	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
11	nsv818441	chr6:86546123-86565943	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Enhancers	lncRNA	n/a	inside rSNPs	diseases
12	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
13	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs57016132	SNHG5	cis	Esophagus Mucosa	GTEx
rs57016132	SNHG5	cis	Esophagus Muscularis	GTEx
rs57016132	SNHG5	cis	Nerve Tibial	GTEx
rs57016132	SNHG5	cis	Artery Aorta	GTEx
rs57016132	SNHG5	cis	lung	GTEx
rs57016132	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs57016132	SNHG5	cis	Artery Tibial	GTEx
rs57016132	SNHG5	cis	Adipose Subcutaneous	GTEx
rs57016132	SNHG5	cis	Whole Blood	GTEx
rs57016132	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs57016132	SNHG5	cis	Thyroid	GTEx
rs57016132	SNHG5	cis	Heart Left Ventricle	GTEx
rs57016132	SNHG5	cis	Muscle Skeletal	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86546800-86556800	Weak transcription	Right Atrium	heart
2	chr6:86551400-86552800	Enhancers	Dnd41	blood
3	chr6:86552400-86552600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
4	chr6:86552400-86552600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:86552400-86552600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:86552400-86552600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:86552400-86552600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:86552400-86552600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
9	chr6:86552400-86552600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
10	chr6:86552400-86552600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
11	chr6:86552400-86552600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:86552400-86552600	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
13	chr6:86552400-86552600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
14	chr6:86552400-86552600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:86552400-86552600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
16	chr6:86552400-86552600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:86552400-86552600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
18	chr6:86552400-86552600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
19	chr6:86552400-86552600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:86552400-86552600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
21	chr6:86552400-86552600	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
22	chr6:86552400-86552600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:86552400-86552600	ZNF genes & repeats	Liver	Liver
24	chr6:86552400-86552600	ZNF genes & repeats	Brain Angular Gyrus	brain
25	chr6:86552400-86552600	ZNF genes & repeats	Brain Anterior Caudate	brain
26	chr6:86552400-86552600	ZNF genes & repeats	Brain Hippocampus Middle	brain
27	chr6:86552400-86552600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
28	chr6:86552400-86552600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:86552400-86552600	ZNF genes & repeats	Brain Substantia Nigra	brain
30	chr6:86552400-86552600	ZNF genes & repeats	Colon Smooth Muscle	Colon
31	chr6:86552400-86552600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
32	chr6:86552400-86552600	Enhancers	Fetal Heart	heart
33	chr6:86552400-86552600	ZNF genes & repeats	Stomach Mucosa	stomach
34	chr6:86552400-86552600	Flanking Bivalent TSS/Enh	NH-A	brain

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