Variant report

Variant	rs4348724
Chromosome Location	chr1:210666568-210666569
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10746426	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10863839	0.83[CHD][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10863840	0.81[EUR][1000 genomes]
rs11119521	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs11119522	0.95[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs11119523	0.83[EUR][1000 genomes]
rs11582700	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12049235	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12408469	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12411254	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs12728693	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12733171	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12759944	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17188260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2473623	0.94[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs4500315	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4545340	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs4622068	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4844530	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845038	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7544655	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[EUR][1000 genomes];0.88[ASN][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	nsv4376	chr1:210627620-210672326	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv873147	chr1:210665583-210696806	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4348724	KCNH1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210639400-210668200	Weak transcription	Primary T cells from cord blood	blood
2	chr1:210643200-210674000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:210653800-210678800	Weak transcription	HSMM	muscle
4	chr1:210657000-210669600	Weak transcription	Brain Substantia Nigra	brain
5	chr1:210663600-210669600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:210663600-210672400	Weak transcription	HSMMtube	muscle
7	chr1:210664800-210669000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:210666000-210667600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:210666000-210669000	Weak transcription	Osteobl	bone

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