Variant report

Variant	rs13053449
Chromosome Location	chr22:33462739-33462740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11704339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11914139	0.83[AFR][1000 genomes]
rs12483802	0.85[CHB][hapmap]
rs12484484	0.86[ASN][1000 genomes]
rs12484648	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs13057082	0.80[AFR][1000 genomes]
rs13057573	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16991758	0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4499532	0.90[AFR][1000 genomes]
rs5754403	0.86[AFR][1000 genomes]
rs5998709	0.81[CHB][hapmap]
rs5998711	0.81[CHB][hapmap]
rs5998714	0.82[CHB][hapmap];0.84[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	nsv531568	chr22:33336868-33480272	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv531587	chr22:33346710-33809338	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1067068	chr22:33452180-33851033	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
5	esv2762120	chr22:33458712-33470321	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv528534	chr22:33459131-33469031	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13053449	TTC28AS	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33454800-33465000	Weak transcription	Fetal Brain Female	brain
2	chr22:33460000-33462800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr22:33460000-33462800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr22:33460200-33462800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr22:33462400-33463200	Enhancers	H1 Cell Line	embryonic stem cell
6	chr22:33462400-33463200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr22:33462600-33462800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr22:33462600-33463000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr22:33462600-33463200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
10	chr22:33462600-33463200	Enhancers	HUES64 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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