Variant report

Variant	rs9960539
Chromosome Location	chr18:24717826-24717827
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs16943240	1.00[AMR][1000 genomes]
rs2339259	0.81[ASN][1000 genomes]
rs28374128	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28377196	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28407882	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28421022	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28422861	0.91[ASN][1000 genomes]
rs28430781	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28441579	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28447060	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28527345	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28540832	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28592609	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28607703	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28625571	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28626613	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28628505	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28636962	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28638047	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28655160	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28658184	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28659873	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28666617	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28669309	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28675069	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28689713	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28690572	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28693844	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28713375	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28774693	0.81[ASN][1000 genomes]
rs62082922	0.91[ASN][1000 genomes]
rs73404849	0.81[ASN][1000 genomes]
rs9944690	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9946111	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9947740	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9947754	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9948063	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9948516	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9948801	1.00[AMR][1000 genomes]
rs9948956	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9949069	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9949945	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9950392	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9950774	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9950985	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9951105	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9951527	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9951666	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9951886	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9952545	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9952700	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9953272	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9954010	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9955379	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9955513	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9955608	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9955617	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9957189	1.00[AMR][1000 genomes]
rs9957834	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9958309	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9958520	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9958672	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9958959	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9959209	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9959230	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9959270	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9959345	0.81[ASN][1000 genomes]
rs9959436	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9959629	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9959749	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9962767	0.81[ASN][1000 genomes]
rs9963374	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9963925	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9965760	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9966121	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][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	nsv1067103	chr18:24524011-24760469	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv543668	chr18:24524011-24760469	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv909473	chr18:24655235-24792075	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv909474	chr18:24683823-24832023	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv909475	chr18:24687324-24776226	Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv530515	chr18:24704459-24883897	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:24711800-24718200	Weak transcription	Spleen	Spleen
2	chr18:24715600-24718400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:24716400-24718000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr18:24716400-24718400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr18:24716400-24718600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr18:24716400-24727400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr18:24716600-24718000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr18:24716600-24718000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr18:24716600-24718200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr18:24716600-24721000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr18:24716600-24722600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr18:24716600-24722600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr18:24716600-24723600	Weak transcription	Gastric	stomach
14	chr18:24716600-24724000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr18:24716600-24730200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr18:24717400-24718200	Enhancers	Pancreas	Pancrea
17	chr18:24717400-24718400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr18:24717600-24718200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr18:24717600-24718800	Enhancers	HepG2	liver
20	chr18:24717600-24719000	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr18:24717800-24718000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr18:24717800-24718000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr18:24717800-24718000	Enhancers	Left Ventricle	heart
24	chr18:24717800-24719000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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