Variant report

Variant	rs1380478
Chromosome Location	chr5:113805362-113805363
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:26)

rs_ID	r²[population]
rs11241279	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11241280	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11241281	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11738819	0.83[ASW][hapmap];0.81[LWK][hapmap]
rs11741945	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11745974	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12153735	0.91[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.83[ASN][1000 genomes]
rs12187240	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12516617	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12516818	0.84[JPT][hapmap]
rs13168840	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13188074	0.83[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs13188819	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13357700	0.84[CHB][hapmap]
rs1364934	1.00[CEU][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1380477	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1459780	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1459781	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]
rs17136633	0.84[JPT][hapmap]
rs1895776	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1993657	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs34333534	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34565875	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36083903	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6884289	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72801872	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[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	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
3	nsv830452	chr5:113798617-113975228	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1380478	KCNN2	cis	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:113793600-113812800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr5:113793800-113812800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:113794200-113808600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:113794200-113813400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:113797000-113809800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:113800200-113813600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:113800400-113807600	Weak transcription	Liver	Liver
8	chr5:113800400-113811000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:113801000-113807400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:113803200-113816000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:113803600-113808600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:113803800-113807600	Weak transcription	Pancreas	Pancrea
13	chr5:113804600-113805800	Enhancers	Fetal Brain Male	brain
14	chr5:113805200-113805600	Weak transcription	Fetal Brain Female	brain

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