Variant report

Variant	rs13197633
Chromosome Location	chr6:28174757-28174758
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:28154956..28156603-chr6:28174738..28177213,2	K562	blood:
2	chr6:28170074..28175450-chr6:28180913..28183647,5	K562	blood:
3	chr6:28174435..28176569-chr6:28303412..28304973,2	MCF-7	breast:
4	chr6:28174526..28176071-chr6:28185476..28187807,2	MCF-7	breast:
5	chr6:28170099..28172681-chr6:28173612..28177819,3	K562	blood:
6	chr6:28109242..28110938-chr6:28172802..28175131,2	MCF-7	breast:
7	chr6:28172570..28175998-chr6:28183959..28188768,7	K562	blood:
8	chr6:28154709..28159711-chr6:28172250..28177968,6	K562	blood:
9	chr6:28174164..28176650-chr6:28369447..28371283,2	K562	blood:
10	chr6:28166299..28169743-chr6:28173090..28175496,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000218016	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs13190888	0.88[EUR][1000 genomes]
rs13191786	0.93[EUR][1000 genomes]
rs13195291	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13197176	1.00[AMR][1000 genomes]
rs13197574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13198809	0.93[EUR][1000 genomes]
rs13200214	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13201308	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13201681	0.93[EUR][1000 genomes]
rs13203816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13204012	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13205211	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13205911	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13207345	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13208096	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13211507	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13213152	0.83[CEU][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13213986	0.83[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13214023	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13217619	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13217984	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs149943	0.83[CEU][hapmap]
rs149990	0.83[CEU][hapmap]
rs202906	0.80[CEU][hapmap]
rs2232423	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs2232426	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs2232429	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs33932084	0.91[EUR][1000 genomes]
rs34166054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34218844	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34243448	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34371502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34396849	0.93[EUR][1000 genomes]
rs34505829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34546986	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34588114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34661125	0.93[EUR][1000 genomes]
rs34691223	0.93[EUR][1000 genomes]
rs34765154	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34832585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34871267	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34878803	0.93[EUR][1000 genomes]
rs34950484	0.93[EUR][1000 genomes]
rs35001169	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35016036	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs35017208	0.93[EUR][1000 genomes]
rs35030260	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs35072899	0.93[EUR][1000 genomes]
rs35098436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35345226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35353359	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs35656932	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35744819	0.93[EUR][1000 genomes]
rs35749575	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35781323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35883476	0.89[EUR][1000 genomes]
rs35902873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35952432	0.83[EUR][1000 genomes]
rs36092177	0.89[EUR][1000 genomes]
rs56075693	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs56189111	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs66886492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67297533	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67340775	0.91[EUR][1000 genomes]
rs67381177	0.93[EUR][1000 genomes]
rs67981811	0.89[EUR][1000 genomes]
rs67998226	0.93[EUR][1000 genomes]
rs68188794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71537572	1.00[AFR][1000 genomes]
rs71559070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71559072	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72846780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72846794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72854513	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7752448	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883514	chr6:28155418-28185726	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv883515	chr6:28156476-28181675	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv883516	chr6:28156476-28185726	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13197633	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13197633	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13197633	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs13197633	AL022393.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28173800-28174800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:28174000-28176400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr6:28174200-28174800	Enhancers	Duodenum Mucosa	Duodenum
4	chr6:28174200-28174800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
5	chr6:28174200-28174800	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr6:28174200-28176400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
7	chr6:28174600-28176400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:28174600-28176600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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