Variant report

Variant	rs13080905
Chromosome Location	chr3:119192709-119192710
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119181220..119185390-chr3:119190378..119193969,7	MCF-7	breast:
2	chr3:119182314..119183843-chr3:119192705..119195422,2	MCF-7	breast:
3	chr3:119186715..119189334-chr3:119191360..119193193,3	K562	blood:
4	chr3:119191895..119193509-chr3:119199992..119202756,2	K562	blood:
5	chr3:119181591..119184535-chr3:119190815..119193290,2	K562	blood:
6	chr3:119187316..119189063-chr3:119192392..119193992,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163389	Chromatin interaction
ENSG00000176142	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1060569	0.94[ASN][1000 genomes]
rs1797839	0.85[ASN][1000 genomes]
rs1900742	0.98[ASN][1000 genomes]
rs1919586	0.98[ASN][1000 genomes]
rs1919590	0.98[ASN][1000 genomes]
rs1967621	0.94[ASN][1000 genomes]
rs1976919	0.94[ASN][1000 genomes]
rs2177812	0.94[ASN][1000 genomes]
rs3732413	0.98[ASN][1000 genomes]
rs3814397	0.85[ASN][1000 genomes]
rs4687855	0.98[ASN][1000 genomes]
rs4687860	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688005	0.98[ASN][1000 genomes]
rs4688007	0.98[ASN][1000 genomes]
rs4688008	0.94[ASN][1000 genomes]
rs4688012	0.94[ASN][1000 genomes]
rs4688014	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6414282	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6414283	0.98[ASN][1000 genomes]
rs6438528	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438529	0.98[ASN][1000 genomes]
rs6438530	0.98[ASN][1000 genomes]
rs6438531	0.98[ASN][1000 genomes]
rs6438535	0.94[ASN][1000 genomes]
rs6777535	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6778945	0.87[ASN][1000 genomes]
rs6794822	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6796970	0.98[ASN][1000 genomes]
rs71618795	0.82[EUR][1000 genomes]
rs727905	0.98[ASN][1000 genomes]
rs7430798	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621259	0.94[ASN][1000 genomes]
rs7628626	0.94[ASN][1000 genomes]
rs7630587	0.98[ASN][1000 genomes]
rs7642502	0.94[ASN][1000 genomes]
rs9289129	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809155	0.98[ASN][1000 genomes]
rs9836627	0.94[ASN][1000 genomes]
rs9850447	0.87[ASN][1000 genomes]
rs9867768	0.87[ASN][1000 genomes]
rs9873196	0.94[ASN][1000 genomes]
rs9874480	0.98[ASN][1000 genomes]
rs9877854	0.94[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13080905	KTELC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119188400-119216200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:119188400-119216800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:119188600-119198000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:119188600-119216200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:119188800-119196200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:119188800-119216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:119189000-119193600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:119189000-119196000	Weak transcription	Small Intestine	intestine
9	chr3:119189000-119196600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:119189000-119196800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:119189000-119197000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:119189000-119198000	Weak transcription	HSMM	muscle
13	chr3:119189000-119198200	Weak transcription	NH-A	brain
14	chr3:119189000-119199200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:119189000-119204400	Weak transcription	NHDF-Ad	bronchial
16	chr3:119189000-119216200	Weak transcription	Stomach Mucosa	stomach
17	chr3:119189000-119216200	Weak transcription	HUVEC	blood vessel
18	chr3:119189000-119216600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:119189200-119196000	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:119189200-119199000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:119189200-119199600	Weak transcription	HMEC	breast
22	chr3:119189200-119203000	Weak transcription	Fetal Kidney	kidney
23	chr3:119189400-119201800	Strong transcription	Fetal Stomach	stomach
24	chr3:119189600-119192800	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:119189600-119193600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:119189600-119205400	Weak transcription	Hela-S3	cervix
27	chr3:119189600-119209200	Strong transcription	Primary B cells from cord blood	blood
28	chr3:119189600-119211800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr3:119189600-119211800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr3:119189800-119193000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:119189800-119194200	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:119189800-119194400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:119189800-119198800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:119189800-119199000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:119189800-119200800	Strong transcription	Fetal Thymus	thymus
36	chr3:119189800-119210000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:119189800-119211400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:119189800-119212200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr3:119189800-119216000	Weak transcription	Fetal Heart	heart
40	chr3:119190000-119193200	Strong transcription	Placenta	Placenta
41	chr3:119190000-119193400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:119190000-119193400	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:119190000-119194000	Strong transcription	Adipose Nuclei	Adipose
44	chr3:119190000-119194400	Strong transcription	Liver	Liver
45	chr3:119190000-119195000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:119190000-119196000	Weak transcription	Colonic Mucosa	Colon
47	chr3:119190000-119201200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:119190000-119201800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:119190000-119202000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:119190000-119211800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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