Variant report

Variant	rs3797566
Chromosome Location	chr5:115234761-115234762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115232531..115235335-chr5:115239466..115241502,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10039749	0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10050876	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10075784	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10751460	0.84[AFR][1000 genomes]
rs11241337	0.81[CHB][hapmap];0.84[CHD][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs12188972	0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs12332653	0.81[CHB][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12513891	0.81[CHB][hapmap]
rs12514553	0.86[AFR][1000 genomes]
rs12519850	0.86[ASN][1000 genomes]
rs12520442	0.86[ASN][1000 genomes]
rs12523122	0.86[ASN][1000 genomes]
rs152368	0.81[CHB][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap]
rs152397	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap]
rs171809	0.82[JPT][hapmap]
rs2080902	0.83[AFR][1000 genomes]
rs26529	0.81[CHB][hapmap]
rs26538	0.86[CHB][hapmap]
rs35238578	0.82[ASN][1000 genomes]
rs3733902	0.89[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3756555	0.81[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3797564	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3797565	0.86[ASN][1000 genomes]
rs3797567	0.85[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.80[ASN][1000 genomes]
rs3797568	0.86[CHB][hapmap];0.81[CHD][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs3797569	0.81[CHB][hapmap]
rs41332950	0.90[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4143542	0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs58463583	0.89[ASN][1000 genomes]
rs6880372	0.82[ASN][1000 genomes]
rs71581217	0.86[ASN][1000 genomes]
rs7708164	0.88[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723291	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv3401617	chr5:115205732-115238678	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv1027418	chr5:115206256-115446861	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv515611	chr5:115208843-115428381	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1021968	chr5:115213162-115426468	Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1024008	chr5:115222974-115431050	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1027117	chr5:115222974-115442883	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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	23 gene(s)	inside rSNPs	diseases
9	esv2763487	chr5:115222986-115442895	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv462400	chr5:115223504-115428381	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv599478	chr5:115223504-115428381	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv1030480	chr5:115228889-115446861	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	esv3441679	chr5:115230797-115238631	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv599479	chr5:115233116-115450969	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3797566	KCNN2	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115189800-115235800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr5:115193200-115239000	Weak transcription	Gastric	stomach
3	chr5:115195400-115263200	Weak transcription	Aorta	Aorta
4	chr5:115205600-115254200	Weak transcription	Small Intestine	intestine
5	chr5:115207600-115238400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr5:115207600-115239200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:115207600-115244600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr5:115207600-115253800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:115207600-115254600	Weak transcription	Fetal Kidney	kidney
10	chr5:115207800-115250800	Weak transcription	Adipose Nuclei	Adipose
11	chr5:115207800-115254000	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:115208000-115253400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr5:115208200-115236000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:115208600-115235600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr5:115212000-115236000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr5:115212600-115238200	Weak transcription	Dnd41	blood
17	chr5:115218600-115253000	Weak transcription	Placenta	Placenta
18	chr5:115218800-115253600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr5:115219000-115252800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:115219200-115252800	Weak transcription	Pancreas	Pancrea
21	chr5:115219200-115253200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:115219400-115236200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr5:115219400-115246800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:115219400-115251000	Weak transcription	Fetal Lung	lung
25	chr5:115219400-115252600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:115219600-115256000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:115221400-115253800	Weak transcription	Fetal Stomach	stomach
28	chr5:115221400-115254400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:115222000-115252800	Weak transcription	Fetal Intestine Small	intestine
30	chr5:115225600-115253200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:115228000-115249200	Weak transcription	HSMMtube	muscle
32	chr5:115230200-115254000	Weak transcription	Ovary	ovary
33	chr5:115230600-115250200	Weak transcription	Liver	Liver
34	chr5:115231600-115245800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:115231600-115247200	Weak transcription	NHDF-Ad	bronchial
36	chr5:115232200-115235000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:115233000-115236600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:115233200-115235000	Strong transcription	Fetal Intestine Large	intestine
39	chr5:115233600-115234800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr5:115233600-115234800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:115233600-115234800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:115233600-115235000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:115233600-115235200	Strong transcription	Fetal Muscle Leg	muscle
44	chr5:115233800-115234800	Enhancers	NHEK	skin
45	chr5:115234000-115234800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:115234000-115234800	Strong transcription	GM12878-XiMat	blood
47	chr5:115234000-115235000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:115234000-115235000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr5:115234000-115235000	Strong transcription	HUVEC	blood vessel
50	chr5:115234000-115235000	Enhancers	NH-A	brain

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