Variant report

Variant	rs9534860
Chromosome Location	chr13:48478037-48478038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11617530	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11620507	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1324801	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1324802	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1408618	0.89[ASN][1000 genomes]
rs1555723	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1555724	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1571256	0.82[JPT][hapmap]
rs1924811	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1974040	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2147502	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2148246	0.83[JPT][hapmap]
rs2148938	0.83[JPT][hapmap]
rs2274189	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406690	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2406709	0.83[JPT][hapmap]
rs28874956	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4142533	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4369555	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs4606606	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4941616	0.89[ASN][1000 genomes]
rs4941623	0.83[JPT][hapmap]
rs4942712	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4942713	0.89[ASN][1000 genomes]
rs4942717	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4942718	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55633570	0.83[ASN][1000 genomes]
rs61972224	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73187725	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7324484	0.82[JPT][hapmap]
rs7329550	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7330169	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7337764	0.89[ASN][1000 genomes]
rs7981303	0.87[ASN][1000 genomes]
rs7998090	0.89[ASN][1000 genomes]
rs9526406	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526407	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526410	0.81[ASN][1000 genomes]
rs9526411	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526414	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526416	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9526442	0.83[JPT][hapmap]
rs9526443	0.83[JPT][hapmap]
rs9534851	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9534856	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534857	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534859	0.89[ASN][1000 genomes]
rs9534861	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9534862	0.89[ASN][1000 genomes]
rs9534863	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534867	0.88[ASN][1000 genomes]
rs9534888	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs9534895	0.84[ASN][1000 genomes]
rs9534900	0.83[ASN][1000 genomes]
rs9534937	0.83[JPT][hapmap]
rs9534939	0.82[JPT][hapmap]
rs9534944	0.90[JPT][hapmap]
rs9534947	0.90[JPT][hapmap]
rs9562775	0.81[ASN][1000 genomes]
rs9567941	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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	esv3510679	chr13:48236624-48498185	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3510680	chr13:48236624-48498185	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv1803690	chr13:48470681-48508091	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48451000-48480200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr13:48461000-48478200	Weak transcription	Left Ventricle	heart
3	chr13:48465000-48484000	Weak transcription	Primary T cells from cord blood	blood
4	chr13:48465200-48478200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr13:48468600-48485600	Weak transcription	Gastric	stomach
6	chr13:48468800-48479600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr13:48468800-48482400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr13:48469000-48478200	Weak transcription	Esophagus	oesophagus
9	chr13:48472000-48482200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:48472200-48482400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr13:48472200-48482400	Weak transcription	NHEK	skin
12	chr13:48472200-48491400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr13:48476000-48479800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr13:48476200-48478400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr13:48477000-48506400	Weak transcription	Psoas Muscle	Psoas
16	chr13:48477200-48478200	Enhancers	NHLF	lung
17	chr13:48478000-48478200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:48478000-48478200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr13:48478000-48478200	Active TSS	Hela-S3	cervix
20	chr13:48478000-48478400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr13:48478000-48478400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr13:48478000-48478400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr13:48478000-48478400	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr13:48478000-48478400	Enhancers	NH-A	brain
25	chr13:48478000-48478600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr13:48478000-48478600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:48478000-48478600	Active TSS	Duodenum Mucosa	Duodenum
28	chr13:48478000-48478600	Active TSS	Placenta	Placenta
29	chr13:48478000-48478600	Active TSS	Osteobl	bone
30	chr13:48478000-48478800	Active TSS	Adipose Nuclei	Adipose
31	chr13:48478000-48478800	Active TSS	Ovary	ovary
32	chr13:48478000-48478800	Active TSS	K562	blood
33	chr13:48478000-48479000	Active TSS	Monocytes-CD14+_RO01746	blood
34	chr13:48478000-48479400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr13:48478000-48479600	Enhancers	HUVEC	blood vessel

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