Variant report

Variant	rs13139538
Chromosome Location	chr4:96098320-96098321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10004711	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10155123	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10155222	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10212627	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10516958	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11097456	0.86[EUR][1000 genomes]
rs11097458	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12506402	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12640643	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12644188	0.89[EUR][1000 genomes]
rs12650281	0.89[EUR][1000 genomes]
rs1365691	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1369085	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1434535	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1434536	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1434538	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1434539	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1540403	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17348139	0.88[EUR][1000 genomes]
rs1813074	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1863654	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2114533	0.80[EUR][1000 genomes]
rs2162450	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2241743	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2241744	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3755876	0.89[EUR][1000 genomes]
rs3775042	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3796437	0.89[EUR][1000 genomes]
rs3796443	0.89[EUR][1000 genomes]
rs3857227	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3857228	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58399580	0.88[EUR][1000 genomes]
rs60472405	0.88[EUR][1000 genomes]
rs6815969	0.82[EUR][1000 genomes]
rs7693146	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7694131	0.89[EUR][1000 genomes]
rs7694531	0.82[ASN][1000 genomes]
rs965823	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs975608	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs989383	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9992669	0.85[EUR][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	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv492312	chr4:95823124-96128327	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv830011	chr4:95947560-96103934	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv594907	chr4:95975470-96170439	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:96059800-96100400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:96080400-96098600	Weak transcription	Fetal Kidney	kidney
3	chr4:96084600-96111800	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:96084800-96099800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:96087600-96107000	Weak transcription	A549	lung
6	chr4:96089200-96098400	Weak transcription	Aorta	Aorta
7	chr4:96089200-96098400	Weak transcription	Ovary	ovary
8	chr4:96090600-96098400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:96091000-96111600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:96091400-96109400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:96091600-96098400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:96091800-96098400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:96091800-96098400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:96091800-96098400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:96091800-96098400	Weak transcription	Fetal Lung	lung
16	chr4:96092000-96098400	Weak transcription	Brain Angular Gyrus	brain
17	chr4:96092000-96098400	Weak transcription	Brain Anterior Caudate	brain
18	chr4:96092000-96098400	Weak transcription	Brain Substantia Nigra	brain
19	chr4:96092200-96098400	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:96097600-96098400	Weak transcription	Spleen	Spleen
21	chr4:96097600-96099600	ZNF genes & repeats	Fetal Stomach	stomach
22	chr4:96098000-96098400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
23	chr4:96098000-96099600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:96098000-96100000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:96098000-96127000	Weak transcription	Right Atrium	heart
26	chr4:96098200-96099000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
27	chr4:96098200-96099000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
28	chr4:96098200-96099000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:96098200-96099400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
30	chr4:96098200-96099400	Strong transcription	Stomach Smooth Muscle	stomach
31	chr4:96098200-96099400	ZNF genes & repeats	Dnd41	blood
32	chr4:96098200-96099600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:96098200-96100400	Strong transcription	Brain Cingulate Gyrus	brain

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