Variant report

Variant	rs6123344
Chromosome Location	chr20:52640514-52640515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52640020..52640592-chr20:52673395..52674189,2	MCF-7	breast:
2	chr20:52638922..52641694-chr20:52671102..52673075,2	MCF-7	breast:
3	chr20:52640367..52641889-chr20:52645625..52647973,2	K562	blood:
4	chr20:52637571..52639350-chr20:52639396..52641959,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11905945	0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap];0.88[ASN][1000 genomes]
rs1381983	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1381984	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1557853	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[ASN][1000 genomes]
rs2107327	0.90[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2189502	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2214530	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238701	0.80[ASN][1000 genomes]
rs2276487	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276488	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276489	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276491	0.94[YRI][hapmap]
rs2299699	0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2299701	0.90[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs2299702	0.90[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs2299704	0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap]
rs2299705	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2299707	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2299711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs2299715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34973146	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35883829	0.88[ASN][1000 genomes]
rs6091808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6091811	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6091812	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6097745	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs6123345	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6127060	0.94[YRI][hapmap]
rs6127062	0.81[YRI][hapmap]
rs6127063	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6127065	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6127066	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6127068	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6127073	0.81[YRI][hapmap]
rs67082409	0.98[ASN][1000 genomes]
rs71323984	0.88[ASN][1000 genomes]
rs732344	0.90[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs765348	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
3	esv2763673	chr20:52637074-52668126	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	nsv3419	chr20:52637581-52672115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52618800-52644400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:52631400-52641400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr20:52633800-52641200	Weak transcription	Brain Angular Gyrus	brain
5	chr20:52634800-52645400	Weak transcription	Fetal Lung	lung
6	chr20:52635800-52641800	Enhancers	Brain Substantia Nigra	brain
7	chr20:52636000-52641200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr20:52636600-52640600	Weak transcription	Stomach Mucosa	stomach
9	chr20:52639200-52640800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr20:52639600-52641000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr20:52640000-52640600	Enhancers	Brain Hippocampus Middle	brain
12	chr20:52640200-52641000	Weak transcription	NHDF-Ad	bronchial
13	chr20:52640200-52641200	Weak transcription	Brain Anterior Caudate	brain
14	chr20:52640400-52642200	Strong transcription	Rectal Mucosa Donor 31	rectum

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