Variant report

Variant	rs12153735
Chromosome Location	chr5:113788755-113788756
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11241279	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11241280	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11241281	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11738819	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11741945	0.84[AFR][1000 genomes]
rs11745974	0.91[ASW][hapmap];0.88[CEU][hapmap];0.88[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12187240	0.86[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12516617	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13168840	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13188074	1.00[JPT][hapmap]
rs13188819	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1364934	0.88[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1380477	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1380478	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]
rs1459780	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs1459781	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]
rs1895776	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs34333534	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs34565875	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs36083903	0.89[AFR][1000 genomes]
rs6884289	0.88[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72801872	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[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
rs12153735	KCNN2	cis	lymphoblastoid	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:113786200-113793200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:113786400-113791600	Weak transcription	Brain Hippocampus Middle	brain
3	chr5:113786400-113793000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:113786400-113793000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:113786400-113793000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:113786600-113793200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:113786600-113793200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:113786600-113793400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:113788200-113789000	Enhancers	Fetal Muscle Leg	muscle
10	chr5:113788400-113793200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:113788600-113792800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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