Variant report

Variant	rs7598311
Chromosome Location	chr2:151870187-151870188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:151869309..151871014-chr2:151874369..151876111,2	MCF-7	breast:
2	chr2:151868019..151872391-chr2:151872649..151877183,5	K562	blood:
3	chr2:151867304..151868964-chr2:151869029..151870769,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10497075	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1117292	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11679370	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11680426	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11684685	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1385430	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16829051	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16829172	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17270016	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1843274	0.85[EUR][1000 genomes]
rs4664217	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4664841	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4664890	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62167192	0.81[EUR][1000 genomes]
rs6433059	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6717928	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6735966	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72485577	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72997777	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs757919	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs757920	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7592542	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs974619	0.87[AMR][1000 genomes];0.92[EUR][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	nsv525350	chr2:151711700-152044794	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv523849	chr2:151718133-152143524	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1002140	chr2:151833257-152054910	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv437297	chr2:151869171-151873561	Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7598311	LYPD6	cis	parietal	SCAN
rs7598311	KCNJ3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151843800-151871000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:151865600-151872800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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