Variant report

Variant	rs6049728
Chromosome Location	chr20:24468238-24468239
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11908507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1326304	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6036815	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049719	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6049723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049754	1.00[CHD][hapmap]
rs6049772	1.00[CHD][hapmap]
rs6106889	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6114736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6114748	1.00[CHD][hapmap]
rs7267072	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs73901847	0.83[EUR][1000 genomes]
rs745979	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[EUR][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	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1058146	chr20:24210196-24531087	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv833946	chr20:24320375-24490702	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3323949	chr20:24467852-24472250	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24457600-24470600	Weak transcription	Fetal Brain Female	brain
2	chr20:24459400-24471000	Weak transcription	Fetal Muscle Leg	muscle
3	chr20:24459400-24471800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr20:24459600-24472000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:24460200-24468800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr20:24460200-24469600	Weak transcription	Brain Anterior Caudate	brain
7	chr20:24460200-24471400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr20:24460200-24472600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr20:24460400-24468600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr20:24460400-24469600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr20:24460800-24468400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr20:24460800-24469800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr20:24460800-24483800	Weak transcription	Aorta	Aorta
14	chr20:24461400-24469800	Weak transcription	Fetal Brain Male	brain
15	chr20:24461800-24468600	Weak transcription	Brain Substantia Nigra	brain
16	chr20:24462200-24469000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr20:24462400-24469800	Weak transcription	Fetal Kidney	kidney
18	chr20:24462400-24472600	Weak transcription	Right Atrium	heart
19	chr20:24463200-24469600	Weak transcription	Fetal Lung	lung
20	chr20:24464600-24472000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr20:24465000-24472800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr20:24465200-24469800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr20:24465200-24469800	Weak transcription	Gastric	stomach
24	chr20:24466400-24469400	Weak transcription	Brain Germinal Matrix	brain
25	chr20:24466600-24469800	Enhancers	Fetal Heart	heart
26	chr20:24466800-24469000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr20:24467000-24469800	Weak transcription	Right Ventricle	heart
28	chr20:24467600-24472800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr20:24468000-24468400	Enhancers	Brain Angular Gyrus	brain
30	chr20:24468000-24468400	Strong transcription	Brain Hippocampus Middle	brain
31	chr20:24468000-24468600	Enhancers	Left Ventricle	heart
32	chr20:24468200-24470000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr20:24468200-24470400	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr20:24468200-24470400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr20:24468200-24470400	Genic enhancers	Brain Cingulate Gyrus	brain

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