Variant report

Variant	rs2121594
Chromosome Location	chr6:86576854-86576855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1059306	0.81[CEU][hapmap]
rs10806337	0.81[ASN][1000 genomes]
rs10944137	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[ASN][1000 genomes]
rs10944138	0.85[ASN][1000 genomes]
rs10944144	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10944145	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10944147	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10944151	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10944152	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10944157	0.93[EUR][1000 genomes]
rs10944161	0.81[EUR][1000 genomes]
rs11752180	0.97[EUR][1000 genomes]
rs11752223	0.97[EUR][1000 genomes]
rs11754330	0.82[ASN][1000 genomes]
rs11755642	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[ASN][1000 genomes]
rs11758508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11758864	0.81[EUR][1000 genomes]
rs11759855	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12153887	0.89[EUR][1000 genomes]
rs12154056	0.81[EUR][1000 genomes]
rs12190603	1.00[CEU][hapmap]
rs12191212	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12192546	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[ASN][1000 genomes]
rs12192992	0.81[EUR][1000 genomes]
rs12193904	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs12196377	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12198061	0.91[EUR][1000 genomes]
rs12198557	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12198730	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12199329	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12201571	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12201741	0.84[EUR][1000 genomes]
rs12201992	0.81[EUR][1000 genomes]
rs12202712	0.99[EUR][1000 genomes]
rs12205492	0.82[ASN][1000 genomes]
rs12209668	0.93[EUR][1000 genomes]
rs12211216	0.88[EUR][1000 genomes]
rs12212480	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs12660846	0.97[EUR][1000 genomes]
rs12665464	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs12665516	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12665542	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13199006	0.80[EUR][1000 genomes]
rs13200064	0.82[EUR][1000 genomes]
rs13201730	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13203309	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13203560	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13207173	1.00[CEU][hapmap]
rs13207537	0.91[EUR][1000 genomes]
rs13209671	0.91[EUR][1000 genomes]
rs13209740	0.83[EUR][1000 genomes]
rs13213551	0.80[EUR][1000 genomes]
rs13213603	0.87[EUR][1000 genomes]
rs13216182	0.80[EUR][1000 genomes]
rs13219504	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1335442	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.80[ASN][1000 genomes]
rs1447160	0.88[EUR][1000 genomes]
rs1470531	1.00[CEU][hapmap]
rs16876540	0.81[EUR][1000 genomes]
rs1813001	0.89[EUR][1000 genomes]
rs1838954	0.93[EUR][1000 genomes]
rs1838955	0.93[EUR][1000 genomes]
rs1838958	0.92[EUR][1000 genomes]
rs1838959	0.91[EUR][1000 genomes]
rs1857965	0.81[EUR][1000 genomes]
rs1911553	0.81[EUR][1000 genomes]
rs1995688	0.89[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs2084293	0.93[EUR][1000 genomes]
rs2084294	0.93[EUR][1000 genomes]
rs2084296	0.89[EUR][1000 genomes]
rs2084297	0.88[EUR][1000 genomes]
rs2100109	0.89[EUR][1000 genomes]
rs2166665	0.89[EUR][1000 genomes]
rs2197648	0.89[EUR][1000 genomes]
rs2218594	0.89[EUR][1000 genomes]
rs2225754	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2324842	0.81[EUR][1000 genomes]
rs2324843	0.81[EUR][1000 genomes]
rs2783171	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs2875456	0.84[EUR][1000 genomes]
rs28885198	0.81[EUR][1000 genomes]
rs34492764	0.81[AFR][1000 genomes]
rs34622557	0.81[EUR][1000 genomes]
rs34622605	0.81[ASN][1000 genomes]
rs34765423	0.85[ASN][1000 genomes]
rs35874630	0.84[EUR][1000 genomes]
rs36035797	0.89[EUR][1000 genomes]
rs36053156	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351219	0.81[EUR][1000 genomes]
rs4706246	0.84[EUR][1000 genomes]
rs4706248	0.88[EUR][1000 genomes]
rs4706252	0.90[EUR][1000 genomes]
rs4706253	0.90[EUR][1000 genomes]
rs4706254	0.82[EUR][1000 genomes]
rs4707223	0.81[EUR][1000 genomes]
rs4707229	0.89[EUR][1000 genomes]
rs4707236	0.84[EUR][1000 genomes]
rs4707239	0.80[EUR][1000 genomes]
rs57016132	0.90[EUR][1000 genomes]
rs61119084	0.85[EUR][1000 genomes]
rs6454487	1.00[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap]
rs67024565	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6900436	0.80[EUR][1000 genomes]
rs72907388	0.81[ASN][1000 genomes]
rs7739241	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7742201	0.85[CEU][hapmap];0.87[CHD][hapmap];0.81[TSI][hapmap]
rs7755730	0.97[EUR][1000 genomes]
rs7766645	0.80[EUR][1000 genomes]
rs7771342	0.81[EUR][1000 genomes]
rs9647601	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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
13	nsv463940	chr6:86576854-86648436	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv604095	chr6:86576854-86648436	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv604096	chr6:86576854-86649705	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2121594	SNHG5	cis	Artery Aorta	GTEx
rs2121594	SNHG5	cis	multi-tissue	Pritchard
rs2121594	SNHG5	cis	Nerve Tibial	GTEx
rs2121594	SNHG5	cis	Artery Tibial	GTEx
rs2121594	SNHG5	cis	Esophagus Mucosa	GTEx
rs2121594	SNHG5	cis	Whole Blood	GTEx
rs2121594	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs2121594	C6orf160	cis	lesional skin	skin_eQTL
rs2121594	SNHG5	cis	Adipose Subcutaneous	GTEx
rs2121594	SNHG5	cis	Esophagus Muscularis	GTEx
rs2121594	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs2121594	C6orf160	cis	uninvolved skin	skin_eQTL
rs2121594	SNHG5	cis	Thyroid	GTEx
rs2121594	SNHG5	cis	Muscle Skeletal	GTEx
rs2121594	SNHG5	cis	Heart Left Ventricle	GTEx
rs2121594	SNHG5	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86563200-86577800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:86575000-86577000	Enhancers	H1 Cell Line	embryonic stem cell
3	chr6:86575200-86577200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
4	chr6:86575200-86583400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:86575800-86577200	Active TSS	Fetal Brain Male	brain
6	chr6:86576000-86577000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:86576000-86577200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:86576000-86577200	Flanking Active TSS	Fetal Lung	lung
9	chr6:86576000-86577200	Flanking Active TSS	HepG2	liver
10	chr6:86576000-86577600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:86576200-86577000	Enhancers	Esophagus	oesophagus
12	chr6:86576200-86577000	Enhancers	Left Ventricle	heart
13	chr6:86576200-86577000	Enhancers	Right Atrium	heart
14	chr6:86576200-86577000	Enhancers	Spleen	Spleen
15	chr6:86576200-86577200	Enhancers	Pancreas	Pancrea
16	chr6:86576200-86578000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:86576200-86578200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr6:86576400-86577000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr6:86576400-86577000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:86576400-86577000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:86576400-86577000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:86576400-86577000	Enhancers	Brain Hippocampus Middle	brain
23	chr6:86576400-86577200	Enhancers	Fetal Kidney	kidney
24	chr6:86576400-86578000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:86576400-86579400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr6:86576600-86577000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr6:86576600-86577200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr6:86576600-86577800	Enhancers	Colon Smooth Muscle	Colon
29	chr6:86576800-86577000	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr6:86576800-86577000	Enhancers	Rectal Smooth Muscle	rectum
31	chr6:86576800-86577200	Enhancers	Ovary	ovary
32	chr6:86576800-86577200	Enhancers	Stomach Smooth Muscle	stomach
33	chr6:86576800-86577400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:86576800-86580000	Weak transcription	Psoas Muscle	Psoas

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