Variant report

Variant	rs1459781
Chromosome Location	chr5:113797444-113797445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11241279	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11241280	0.85[AFR][1000 genomes]
rs11241281	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11738819	0.83[ASW][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap]
rs11741945	0.83[AFR][1000 genomes]
rs11745974	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12153735	0.91[ASW][hapmap];0.82[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs12187240	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12516617	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12516818	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs13168840	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13188074	0.94[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs13188819	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1364934	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1380477	0.92[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1380478	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1459780	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17136633	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs1895776	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1993657	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs34333534	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34565875	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs36083903	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4435855	0.81[CHB][hapmap]
rs4705505	0.85[CHB][hapmap]
rs6884289	0.92[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72801872	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830451	chr5:113684301-113829833	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv882729	chr5:113743628-114497708	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1459781	KCNN2	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:113793400-113798600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:113793600-113799400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:113793600-113799400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:113793600-113812800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:113793800-113812800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr5:113794200-113808600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:113794200-113813400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:113794600-113799400	Weak transcription	Liver	Liver
9	chr5:113794800-113798800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr5:113796000-113797600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:113796600-113798200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:113797000-113809800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:113797400-113801000	Weak transcription	Brain Anterior Caudate	brain

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