Variant report

Variant	rs13069980
Chromosome Location	chr3:111466766-111466767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD96-3	chr3:111466665-111467424	NONHSAT091151

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10212300	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10470303	0.91[ASN][1000 genomes]
rs10934106	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934107	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11710738	0.95[ASN][1000 genomes]
rs12490166	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12490595	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496925	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496971	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12497012	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13074817	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079085	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4284954	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4431081	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682057	1.00[ASN][1000 genomes]
rs4682305	0.95[ASN][1000 genomes]
rs62273780	0.95[ASN][1000 genomes]
rs6438003	0.88[EUR][1000 genomes]
rs6438008	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438009	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6764720	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6768713	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6777540	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6784753	0.98[ASN][1000 genomes]
rs6786386	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786612	0.93[ASN][1000 genomes]
rs6790072	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6790079	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792493	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6802995	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7427201	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7609653	0.99[ASN][1000 genomes]
rs7614443	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9818574	0.91[ASN][1000 genomes]
rs9823974	0.91[ASN][1000 genomes]
rs9825915	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9834030	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9838371	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9863403	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9868171	0.95[ASN][1000 genomes]
rs9870823	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111458000-111467000	Weak transcription	Right Ventricle	heart
2	chr3:111458600-111467200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:111458800-111466800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:111462400-111466800	Weak transcription	Liver	Liver
5	chr3:111462600-111467000	Weak transcription	Fetal Kidney	kidney
6	chr3:111462600-111468000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:111462600-111468000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:111463000-111469600	Weak transcription	Adipose Nuclei	Adipose
9	chr3:111463800-111468200	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:111464000-111467000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:111465000-111469200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:111465200-111468000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:111465200-111468200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:111465200-111468400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:111465400-111469600	Weak transcription	A549	lung
16	chr3:111465400-111470400	Weak transcription	Hela-S3	cervix
17	chr3:111466000-111467000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:111466000-111467400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:111466200-111467200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:111466200-111471400	Enhancers	NHEK	skin
21	chr3:111466400-111466800	Enhancers	NHDF-Ad	bronchial
22	chr3:111466400-111467200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:111466400-111467200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:111466400-111467400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:111466400-111467400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:111466400-111467400	Enhancers	Gastric	stomach
27	chr3:111466400-111467400	Enhancers	HMEC	breast
28	chr3:111466400-111467400	Enhancers	NH-A	brain
29	chr3:111466400-111467600	Enhancers	HepG2	liver
30	chr3:111466400-111468200	Enhancers	HUVEC	blood vessel
31	chr3:111466400-111469400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr3:111466400-111469600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:111466400-111471200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:111466400-111471400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:111466600-111467000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:111466600-111467200	Enhancers	Osteobl	bone
37	chr3:111466600-111467400	Enhancers	Stomach Mucosa	stomach
38	chr3:111466600-111471000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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