Variant report

Variant	rs2129773
Chromosome Location	chr15:53853302-53853303
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:9)

rs_ID	r²[population]
rs10220757	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11633531	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12911064	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1906422	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1906427	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774666	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8034897	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9302171	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs957284	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904223	chr15:53665247-54340070	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv904224	chr15:53668018-54210677	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv833009	chr15:53752901-53935303	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv9267	chr15:53821005-54132612	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv569433	chr15:53828686-53860607	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv904225	chr15:53840665-53878948	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
9	nsv569434	chr15:53845097-53860607	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv569435	chr15:53845097-53966805	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53850600-53853800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:53850800-53853600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:53850800-53854000	Enhancers	Fetal Intestine Large	intestine
4	chr15:53850800-53854800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr15:53851200-53853400	Enhancers	Duodenum Mucosa	Duodenum
6	chr15:53851600-53853400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:53852000-53853800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:53852400-53853800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr15:53852400-53854200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:53852600-53853600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr15:53852600-53853600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:53852600-53853600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:53852600-53853600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr15:53852600-53857000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:53852600-53861800	Weak transcription	A549	lung
16	chr15:53852800-53853800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:53852800-53854800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:53853000-53854000	Weak transcription	Liver	Liver
19	chr15:53853000-53856800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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