Variant report

Variant	rs688880
Chromosome Location	chr1:103241009-103241010
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10047217	0.88[JPT][hapmap]
rs12046389	1.00[JPT][hapmap]
rs12143740	1.00[JPT][hapmap]
rs12144670	1.00[JPT][hapmap]
rs1932342	0.83[EUR][1000 genomes]
rs2126642	1.00[JPT][hapmap]
rs2126643	1.00[JPT][hapmap]
rs2199554	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2199555	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2616010	1.00[JPT][hapmap]
rs2616011	1.00[JPT][hapmap]
rs2622865	1.00[JPT][hapmap]
rs2708397	0.82[EUR][1000 genomes]
rs2708398	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767273	1.00[JPT][hapmap]
rs471949	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs472765	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs500936	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511308	0.84[EUR][1000 genomes]
rs514077	0.84[EUR][1000 genomes]
rs514099	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs520747	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs570092	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579692	0.84[EUR][1000 genomes]
rs597499	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618072	0.84[EUR][1000 genomes]
rs620658	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs629282	0.84[EUR][1000 genomes]
rs631137	0.84[EUR][1000 genomes]
rs665275	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6682134	1.00[JPT][hapmap]
rs674479	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687616	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7543705	1.00[JPT][hapmap]

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	nsv462705	chr1:103123803-103267759	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv546923	chr1:103123803-103267759	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv870987	chr1:103155901-103267759	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv462716	chr1:103176592-103259724	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv546924	chr1:103176592-103259724	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv546925	chr1:103176592-103267759	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv546926	chr1:103183066-103267759	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv830882	chr1:103192683-103355802	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv546927	chr1:103199589-103267759	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3403184	chr1:103238964-103241087	Active TSS Flanking Active TSS Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103233200-103243200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:103238600-103241600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:103240600-103241600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:103240600-103241600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:103241000-103241800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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