Variant report

Variant	rs12196175
Chromosome Location	chr6:86779370-86779371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1018184	0.86[EUR][1000 genomes]
rs10498958	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10944161	0.84[EUR][1000 genomes]
rs10944168	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10944169	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10944170	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11755864	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11756615	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11756621	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11758849	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11758864	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11759855	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12154056	0.84[EUR][1000 genomes]
rs12190012	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12190598	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12190735	0.80[AMR][1000 genomes]
rs12192992	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12194747	0.86[EUR][1000 genomes]
rs12196037	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12197883	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12199516	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12199784	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12199832	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12201571	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12201741	0.82[EUR][1000 genomes]
rs12201992	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12205336	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12207305	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12209127	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12212733	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12213149	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12215037	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12215903	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12216203	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12216328	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12661204	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12665321	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13196930	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13199006	0.83[EUR][1000 genomes]
rs13213551	0.83[EUR][1000 genomes]
rs13216182	0.83[EUR][1000 genomes]
rs13217384	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1337843	0.86[EUR][1000 genomes]
rs1337844	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1415753	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1577917	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16876540	0.84[EUR][1000 genomes]
rs1857965	0.84[EUR][1000 genomes]
rs1911553	0.84[EUR][1000 genomes]
rs1962715	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1962716	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1995688	0.84[EUR][1000 genomes]
rs1999852	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2324842	0.84[EUR][1000 genomes]
rs2324843	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2660576	0.85[EUR][1000 genomes]
rs2816815	0.85[EUR][1000 genomes]
rs2875456	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34106666	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34258068	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34300848	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34492764	0.83[EUR][1000 genomes]
rs34581302	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34622557	0.84[EUR][1000 genomes]
rs34852683	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35038582	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35156995	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35385043	0.85[EUR][1000 genomes]
rs35419329	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35738006	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35797755	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36096931	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36138664	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4351219	0.84[EUR][1000 genomes]
rs4706254	0.81[EUR][1000 genomes]
rs4707239	0.83[EUR][1000 genomes]
rs6454513	0.88[EUR][1000 genomes]
rs6454515	0.85[EUR][1000 genomes]
rs68171315	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6914463	0.85[EUR][1000 genomes]
rs6923148	0.99[EUR][1000 genomes]
rs6933377	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6936048	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7747824	0.85[EUR][1000 genomes]
rs7747897	0.86[EUR][1000 genomes]
rs7760207	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7766645	0.83[EUR][1000 genomes]
rs7771342	0.84[EUR][1000 genomes]
rs791856	0.85[EUR][1000 genomes]
rs884841	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs884842	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9353349	0.81[EUR][1000 genomes]
rs955227	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1027719	chr6:86745200-87326311	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1026234	chr6:86745200-87640200	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv532046	chr6:86754494-87615799	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1024339	chr6:86778852-87622650	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1018878	chr6:86778852-87691755	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12196175	SNHG5	cis	lung	GTEx
rs12196175	SNHG5	cis	Thyroid	GTEx
rs12196175	SNHG5	cis	Nerve Tibial	GTEx
rs12196175	SNHG5	cis	Heart Left Ventricle	GTEx
rs12196175	SNHG5	cis	Whole Blood	GTEx
rs12196175	SNHG5	cis	multi-tissue	Pritchard
rs12196175	SNHG5	cis	Esophagus Mucosa	GTEx
rs12196175	SNHG5	cis	Muscle Skeletal	GTEx
rs12196175	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs12196175	SNHG5	cis	Artery Tibial	GTEx
rs12196175	SNHG5	cis	Artery Aorta	GTEx
rs12196175	SNHG5	cis	Esophagus Muscularis	GTEx
rs12196175	SNHG5	cis	Adipose Subcutaneous	GTEx
rs12196175	SNHG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86779000-86779600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:86779000-86779600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:86779000-86779600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:86779200-86779600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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