Variant report

Variant	rs7660636
Chromosome Location	chr4:105869983-105869984
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:105859609..105862391-chr4:105868336..105871291,2	K562	blood:
2	chr4:105868338..105870861-chr4:105885539..105888181,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248242	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10005322	0.93[ASN][1000 genomes]
rs10016801	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10026528	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10032763	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12331635	0.82[AFR][1000 genomes]
rs1388035	0.80[ASN][1000 genomes]
rs1388036	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs1388038	1.00[ASN][1000 genomes]
rs17035104	0.82[ASW][hapmap];0.82[AFR][1000 genomes]
rs17035107	0.82[ASW][hapmap];0.82[AFR][1000 genomes]
rs1994633	0.95[ASN][1000 genomes]
rs1994634	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1994635	1.00[ASN][1000 genomes]
rs2087590	0.95[ASN][1000 genomes]
rs28375724	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28593451	1.00[ASN][1000 genomes]
rs28611049	0.82[AFR][1000 genomes]
rs28821492	0.82[AFR][1000 genomes]
rs3943090	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4698927	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs57379426	0.95[ASN][1000 genomes]
rs58308342	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62329755	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62329756	0.93[ASN][1000 genomes]
rs62331060	1.00[ASN][1000 genomes]
rs62331061	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62331063	1.00[ASN][1000 genomes]
rs62331067	0.82[ASN][1000 genomes]
rs72949461	0.96[ASN][1000 genomes]
rs7690950	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7691125	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7691297	1.00[ASN][1000 genomes]
rs9993343	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3341748	chr4:105569622-105903733	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv3388659	chr4:105613526-105882646	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7660636	SNORD116-29	trans	lymphoblastoid	seeQTL
rs7660636	SNORD50A	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:105863600-105877400	Weak transcription	Liver	Liver
2	chr4:105869200-105870000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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