Variant report

Variant	rs9809960
Chromosome Location	chr3:119111049-119111050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12639070	0.83[ASN][1000 genomes]
rs16829809	0.81[ASN][1000 genomes]
rs17281612	0.83[ASN][1000 genomes]
rs58968288	0.83[ASN][1000 genomes]
rs59333081	0.83[ASN][1000 genomes]
rs59551807	0.83[ASN][1000 genomes]
rs60375691	0.83[ASN][1000 genomes]
rs61740281	0.83[ASN][1000 genomes]
rs6772534	0.81[ASN][1000 genomes]
rs6800924	0.83[ASN][1000 genomes]
rs72968474	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv3962	chr3:119094646-119135321	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9809960	KTELC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119069400-119111400	Weak transcription	Fetal Intestine Small	intestine
2	chr3:119072000-119133800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:119072200-119114200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:119078800-119111400	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:119080000-119145600	Weak transcription	Fetal Kidney	kidney
6	chr3:119081200-119135600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:119081400-119114200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:119082800-119138000	Weak transcription	Small Intestine	intestine
9	chr3:119085200-119139000	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:119088000-119134200	Weak transcription	NHDF-Ad	bronchial
11	chr3:119088200-119122400	Weak transcription	Brain Angular Gyrus	brain
12	chr3:119093000-119116200	Weak transcription	Psoas Muscle	Psoas
13	chr3:119094400-119119600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:119097000-119132600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:119097600-119120600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:119098000-119136800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:119098400-119111400	Weak transcription	Liver	Liver
18	chr3:119098400-119138200	Strong transcription	Adipose Nuclei	Adipose
19	chr3:119098600-119137400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:119099000-119126200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:119099200-119111200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:119099200-119120600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:119099600-119124800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:119099800-119114200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:119099800-119114200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:119100000-119115400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:119100000-119118200	Weak transcription	Fetal Heart	heart
28	chr3:119100000-119132600	Weak transcription	Primary B cells from cord blood	blood
29	chr3:119100200-119114600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:119102600-119133200	Weak transcription	NHLF	lung
31	chr3:119102600-119134800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:119103600-119112000	Weak transcription	GM12878-XiMat	blood
33	chr3:119103600-119112600	Weak transcription	HSMM	muscle
34	chr3:119103800-119118200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:119105200-119112200	Strong transcription	Fetal Stomach	stomach
36	chr3:119105200-119112200	Strong transcription	Lung	lung
37	chr3:119105400-119130000	Weak transcription	Fetal Brain Male	brain
38	chr3:119106400-119131200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr3:119106800-119137400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:119107000-119114600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:119107200-119112200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:119107200-119123000	Strong transcription	HUVEC	blood vessel
43	chr3:119107600-119115000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:119107800-119112200	Strong transcription	Ovary	ovary
45	chr3:119108400-119112200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:119108400-119113200	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:119108400-119113400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:119108400-119114600	Strong transcription	Left Ventricle	heart
49	chr3:119108400-119125600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:119108600-119112800	Strong transcription	Primary T cells from cord blood	blood

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