Variant report

Variant	rs34622605
Chromosome Location	chr6:86456519-86456520
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:86456386-86456586	GM12878	blood:	n/a	n/a
2	RAD21	chr6:86456439-86456585	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr6:86456456-86456565	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:86452591..86454803-chr6:86455984..86458666,2	K562	blood:
2	chr6:86385780..86390752-chr6:86454284..86460508,14	MCF-7	breast:
3	chr6:86351009..86353966-chr6:86455070..86459127,4	MCF-7	breast:

Variant related genes	Relation type
RNU4-72P	TF binding region
ENSG00000135316	Chromatin interaction
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10806337	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10944136	0.97[EUR][1000 genomes]
rs10944137	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10944138	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10944144	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10944145	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10944147	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10944151	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10944152	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11754330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11755642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11758508	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12153887	0.81[EUR][1000 genomes]
rs12190603	0.97[EUR][1000 genomes]
rs12191212	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12192546	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12193904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12196377	0.82[ASN][1000 genomes]
rs12198557	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12198730	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12199329	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12205492	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12211216	0.80[EUR][1000 genomes]
rs12212151	0.87[EUR][1000 genomes]
rs12212480	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12665516	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12665542	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13201730	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13203309	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13203560	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13207173	0.99[EUR][1000 genomes]
rs13219504	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1335442	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1447160	0.80[EUR][1000 genomes]
rs1470531	0.89[EUR][1000 genomes]
rs1813001	0.81[EUR][1000 genomes]
rs2084296	0.81[EUR][1000 genomes]
rs2100109	0.81[EUR][1000 genomes]
rs2121594	0.81[ASN][1000 genomes]
rs2166665	0.81[EUR][1000 genomes]
rs2197648	0.81[EUR][1000 genomes]
rs2218594	0.81[EUR][1000 genomes]
rs2225754	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2324817	0.99[EUR][1000 genomes]
rs34765423	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34795473	0.99[EUR][1000 genomes]
rs36053156	0.81[ASN][1000 genomes]
rs4098044	0.99[EUR][1000 genomes]
rs4707223	0.89[EUR][1000 genomes]
rs4707229	0.81[EUR][1000 genomes]
rs6454487	0.99[EUR][1000 genomes]
rs6454488	0.99[EUR][1000 genomes]
rs66807489	0.96[EUR][1000 genomes]
rs67024565	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6900436	0.91[EUR][1000 genomes]
rs72907388	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9647601	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs34622605	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs34622605	SNHG5	cis	Nerve Tibial	GTEx
rs34622605	SNHG5	cis	Whole Blood	GTEx
rs34622605	SNHG5	cis	Heart Left Ventricle	GTEx
rs34622605	SNHG5	cis	Adipose Subcutaneous	GTEx
rs34622605	SNHG5	cis	Artery Aorta	GTEx
rs34622605	SNHG5	cis	Artery Tibial	GTEx
rs34622605	SNHG5	cis	Esophagus Mucosa	GTEx
rs34622605	SNHG5	cis	Thyroid	GTEx
rs34622605	SNHG5	cis	Esophagus Muscularis	GTEx
rs34622605	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs34622605	SNHG5	cis	multi-tissue	Pritchard
rs34622605	SNHG5	cis	lung	GTEx
rs34622605	SNHG5	cis	Muscle Skeletal	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86455600-86457400	Weak transcription	HepG2	liver
2	chr6:86455600-86458800	Weak transcription	Fetal Intestine Large	intestine
3	chr6:86455600-86460800	Weak transcription	Fetal Intestine Small	intestine
4	chr6:86456400-86457000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:86456400-86457600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:86456400-86457800	Enhancers	Osteobl	bone

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