Variant report

Variant	rs6556809
Chromosome Location	chr5:164563948-164563949
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10078215	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1019444	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10515891	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11135347	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11135353	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11135354	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11135356	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11135357	0.88[EUR][1000 genomes]
rs11135360	0.85[EUR][1000 genomes]
rs12520638	0.96[ASN][1000 genomes]
rs13156646	0.88[EUR][1000 genomes]
rs13160815	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13162946	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13165528	0.82[EUR][1000 genomes]
rs13183298	0.83[ASN][1000 genomes]
rs1363117	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1421678	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1421701	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1421713	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1433004	0.89[CEU][hapmap]
rs17072571	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28450493	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34405444	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4323250	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4362959	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4431365	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4577712	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6870031	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6876275	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6884200	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6895570	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7447491	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766121	0.97[ASN][1000 genomes]
rs7701554	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7717921	0.80[EUR][1000 genomes]
rs7736590	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs885477	0.83[EUR][1000 genomes]
rs969903	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs991328	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv995060	chr5:163660200-164620500	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv528624	chr5:164319435-164701201	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1033866	chr5:164419608-164677758	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1027138	chr5:164563093-164852655	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv537937	chr5:164563093-164852655	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1028006	chr5:164563293-164852516	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv537938	chr5:164563293-164852516	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:164557800-164565000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr5:164557800-164570800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:164558000-164564800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:164558200-164564800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:164558200-164565000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:164562200-164564800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:164562800-164564400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:164562800-164565200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:164563000-164564000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:164563000-164564800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:164563000-164564800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:164563200-164564400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:164563800-164565200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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