Variant report

Variant	rs1344687
Chromosome Location	chr3:134039862-134039863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs13094988	0.80[ASN][1000 genomes]
rs2270733	0.95[ASN][1000 genomes]
rs34426406	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34591691	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34596580	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34688449	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34913236	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35160848	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35369871	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4131649	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4131651	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4234420	0.95[ASN][1000 genomes]
rs4270476	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4437113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4449291	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4470481	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4504146	0.83[ASN][1000 genomes]
rs4510358	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4533618	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4558731	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4574266	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682661	0.95[ASN][1000 genomes]
rs4682663	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55721085	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6774600	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71331752	0.92[ASN][1000 genomes]
rs7374739	0.87[AFR][1000 genomes]
rs7431754	0.95[ASN][1000 genomes]
rs7614238	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621320	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641605	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644134	0.92[ASN][1000 genomes]
rs7652144	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289466	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289467	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863226	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9866886	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1344687	RP11-375I20.6	cis	Thyroid	GTEx
rs1344687	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs1344687	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs1344687	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134034600-134046200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:134034800-134041600	Weak transcription	Pancreas	Pancrea
3	chr3:134034800-134043200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:134034800-134044200	Weak transcription	Right Ventricle	heart
5	chr3:134035000-134041200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:134035000-134044000	Weak transcription	Fetal Heart	heart
7	chr3:134035000-134044200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:134035000-134045000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:134035000-134058800	Weak transcription	Liver	Liver
10	chr3:134036600-134043200	Weak transcription	Lung	lung
11	chr3:134036600-134044200	Weak transcription	Esophagus	oesophagus
12	chr3:134036600-134045000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:134036600-134050600	Weak transcription	Fetal Brain Female	brain
14	chr3:134037000-134042600	Weak transcription	Adipose Nuclei	Adipose
15	chr3:134037200-134042800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:134037200-134043200	Weak transcription	NHDF-Ad	bronchial
17	chr3:134037200-134043400	Weak transcription	HSMMtube	muscle
18	chr3:134037600-134040800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:134038800-134040000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr3:134038800-134040000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:134038800-134040000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:134038800-134040200	Enhancers	HSMM	muscle
23	chr3:134039200-134040000	Enhancers	Placenta Amnion	Placenta Amnion
24	chr3:134039200-134040200	Enhancers	HMEC	breast
25	chr3:134039400-134040000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:134039400-134040000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:134039400-134040000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:134039400-134040000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:134039400-134040000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:134039400-134040000	Enhancers	Placenta	Placenta
31	chr3:134039400-134040000	Enhancers	Gastric	stomach
32	chr3:134039400-134040000	Enhancers	Stomach Mucosa	stomach
33	chr3:134039400-134040000	Enhancers	NH-A	brain
34	chr3:134039400-134040000	Enhancers	NHLF	lung
35	chr3:134039400-134040000	Enhancers	Osteobl	bone
36	chr3:134039400-134041800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:134039600-134040000	Enhancers	H1 Cell Line	embryonic stem cell
38	chr3:134039600-134040000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:134039800-134040800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:134039800-134041600	Weak transcription	A549	lung
41	chr3:134039800-134044000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:134039800-134044200	Weak transcription	Hela-S3	cervix
43	chr3:134039800-134045000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:134039800-134045600	Enhancers	NHEK	skin

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