Variant report

Variant	rs657079
Chromosome Location	chr3:119345950-119345951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119344313..119346275-chr3:119356031..119358042,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1032131	0.98[ASN][1000 genomes]
rs1032132	0.98[ASN][1000 genomes]
rs11710365	1.00[LWK][hapmap]
rs12631518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12638684	0.98[ASN][1000 genomes]
rs12639410	0.98[ASN][1000 genomes]
rs13062086	0.98[ASN][1000 genomes]
rs13318540	0.98[ASN][1000 genomes]
rs1471792	0.98[ASN][1000 genomes]
rs1471793	0.98[ASN][1000 genomes]
rs1877594	0.98[ASN][1000 genomes]
rs1877595	0.98[ASN][1000 genomes]
rs1967051	0.98[ASN][1000 genomes]
rs1967052	0.98[ASN][1000 genomes]
rs2247660	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2280669	0.86[ASN][1000 genomes]
rs2629406	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2670288	0.98[ASN][1000 genomes]
rs3755583	0.98[ASN][1000 genomes]
rs3772132	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4688020	0.98[ASN][1000 genomes]
rs483349	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6799965	0.98[ASN][1000 genomes]
rs6800119	0.92[ASN][1000 genomes]
rs9832300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9834422	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv591363	chr3:119316828-119345950	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv1795621	chr3:119344693-119353995	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs657079	KTELC1	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119322200-119349200	Weak transcription	Gastric	stomach
2	chr3:119340800-119357600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:119341400-119364600	Weak transcription	Liver	Liver
4	chr3:119342400-119346400	Enhancers	GM12878-XiMat	blood
5	chr3:119342600-119346600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:119343200-119349200	Weak transcription	Fetal Intestine Small	intestine
7	chr3:119343800-119349200	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr3:119343800-119351400	Enhancers	Psoas Muscle	Psoas
9	chr3:119344000-119347600	Enhancers	Lung	lung
10	chr3:119344200-119349600	Enhancers	Spleen	Spleen
11	chr3:119344400-119346000	Enhancers	Placenta	Placenta
12	chr3:119344400-119348400	Enhancers	Left Ventricle	heart
13	chr3:119344400-119351000	Weak transcription	Pancreas	Pancrea
14	chr3:119344600-119346600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:119344600-119346800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:119344600-119352000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr3:119344800-119346400	Weak transcription	Ovary	ovary
18	chr3:119344800-119350000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:119345000-119348200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:119345000-119349800	Enhancers	Right Ventricle	heart
21	chr3:119345000-119350000	Enhancers	Adipose Nuclei	Adipose
22	chr3:119345200-119347800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr3:119345200-119348200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:119345200-119349400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:119345200-119350800	Weak transcription	Fetal Heart	heart
26	chr3:119345200-119357600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:119345400-119347800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:119345400-119347800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:119345400-119348000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:119345400-119348400	Enhancers	Primary B cells from peripheral blood	blood
31	chr3:119345400-119348400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr3:119345400-119349000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:119345600-119346200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr3:119345600-119347200	Enhancers	Primary hematopoietic stem cells	blood
35	chr3:119345600-119347200	Enhancers	HUVEC	blood vessel
36	chr3:119345600-119347800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr3:119345800-119346000	Enhancers	Fetal Thymus	thymus
38	chr3:119345800-119346200	Weak transcription	Right Atrium	heart
39	chr3:119345800-119347400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:119345800-119347600	Enhancers	Primary T cells fromperipheralblood	blood
41	chr3:119345800-119348200	Enhancers	Primary B cells from cord blood	blood
42	chr3:119345800-119349200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr3:119345800-119355200	Weak transcription	Brain Hippocampus Middle	brain

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