Variant report

Variant	rs6036670
Chromosome Location	chr20:24145833-24145834
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24139018..24140898-chr20:24143950..24146165,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs127801	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes]
rs1496400	0.84[CEU][hapmap]
rs1587200	0.84[CEU][hapmap]
rs1884521	0.88[ASN][1000 genomes]
rs2013711	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2208013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs224151	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs224153	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs224154	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2749424	0.84[AMR][1000 genomes]
rs2890401	0.84[ASN][1000 genomes]
rs576373	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6036665	0.84[ASN][1000 genomes]
rs6036668	0.85[ASN][1000 genomes]
rs6049429	0.84[ASN][1000 genomes]
rs6049432	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs6049433	0.81[CEU][hapmap]
rs6049434	0.84[ASN][1000 genomes]
rs6049435	0.84[ASN][1000 genomes]
rs6049439	0.84[ASN][1000 genomes]
rs6049443	0.84[ASN][1000 genomes]
rs6049446	0.85[ASN][1000 genomes]
rs6049453	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6049454	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6049455	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6049458	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6049460	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6049461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6049467	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6083394	0.84[ASN][1000 genomes]
rs6083397	0.84[ASN][1000 genomes]
rs6114503	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6114507	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6114508	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6114509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs761868	0.88[CEU][hapmap];0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs761869	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs761870	0.84[ASN][1000 genomes]
rs85687	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs85689	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs910780	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs910781	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3328348	chr20:24095746-24285830	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6036670	GGTLC1	cis	parietal	SCAN
rs6036670	CST9	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24134400-24146800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:24144000-24146200	Enhancers	HUVEC	blood vessel
3	chr20:24145200-24146800	Enhancers	Colon Smooth Muscle	Colon
4	chr20:24145200-24147400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr20:24145200-24147400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr20:24145400-24146400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr20:24145400-24147800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr20:24145400-24148000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr20:24145600-24146400	Enhancers	Fetal Kidney	kidney
10	chr20:24145800-24146400	Enhancers	Fetal Stomach	stomach
11	chr20:24145800-24147200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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