Variant report

Variant	rs1880218
Chromosome Location	chr3:61158423-61158424
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10866044	0.84[CHD][hapmap]
rs11707813	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs11711938	0.81[ASN][1000 genomes]
rs11716189	0.81[ASN][1000 genomes]
rs12494967	1.00[ASW][hapmap];0.82[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12632475	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12633494	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12637792	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs13087102	0.81[ASN][1000 genomes]
rs13323559	0.81[ASN][1000 genomes]
rs1403968	0.86[ASN][1000 genomes]
rs1851784	0.82[CEU][hapmap]
rs4688324	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61440939	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876185	0.84[CHD][hapmap]
rs9877396	0.81[CHD][hapmap]
rs9877573	0.81[ASN][1000 genomes]
rs9881340	0.81[ASN][1000 genomes]
rs9917837	0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv948633	chr3:60993915-61171279	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	esv2757873	chr3:61019003-61185558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv590425	chr3:61132698-61186550	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv1012435	chr3:61136874-61181318	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv1014142	chr3:61136874-61184782	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	esv2756994	chr3:61144427-61220809	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv3356549	chr3:61158377-61158443	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
14	nsv527725	chr3:61158423-61160226	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1880218	KCNN2	trans	lymphoblastoid	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61149400-61159400	Weak transcription	Fetal Intestine Large	intestine
2	chr3:61151200-61188000	Weak transcription	Primary T cells from cord blood	blood
3	chr3:61154200-61160400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:61156200-61159400	Weak transcription	Liver	Liver
5	chr3:61157200-61160000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:61157400-61158800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:61157400-61159600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:61157400-61161200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:61157600-61161000	Enhancers	Primary hematopoietic stem cells	blood
10	chr3:61158000-61158600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr3:61158000-61158600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr3:61158000-61158600	Enhancers	Dnd41	blood
13	chr3:61158000-61158800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:61158000-61159600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:61158200-61158600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr3:61158200-61158800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:61158200-61158800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:61158200-61158800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:61158200-61159400	Enhancers	GM12878-XiMat	blood
20	chr3:61158400-61158800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:61158400-61158800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr3:61158400-61158800	Enhancers	Brain Substantia Nigra	brain
23	chr3:61158400-61158800	Enhancers	Pancreas	Pancrea
24	chr3:61158400-61159000	Enhancers	Gastric	stomach

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