Variant report

Variant	rs2462970
Chromosome Location	chr17:38871049-38871050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38870270..38871800-chr17:38876957..38879184,2	K562	blood:
2	chr17:38800758..38806200-chr17:38867662..38875106,8	MCF-7	breast:
3	chr17:38864332..38866503-chr17:38870662..38872459,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073584	Chromatin interaction
ENSG00000229028	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2008469	0.80[ASN][1000 genomes]
rs2014704	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2109223	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2159430	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2253717	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2315020	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2429549	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2462962	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462963	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462964	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2469818	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4890119	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4890122	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58630924	0.90[ASN][1000 genomes]
rs6503549	0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs7209467	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs7209735	0.81[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs7212255	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223332	0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7223354	0.81[ASN][1000 genomes]
rs723729	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs726848	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726849	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs758630	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068721	0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs8076587	0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs917593	0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs917595	0.88[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs9675112	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs9896791	0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2462970	KRT222	cis	Nerve Tibial	GTEx
rs2462970	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs2462970	KRT24	cis	Esophagus Mucosa	GTEx
rs2462970	CCR7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38854000-38875800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:38860000-38890200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:38864800-38874800	Weak transcription	Placenta Amnion	Placenta Amnion

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