Variant report

Variant	rs35715914
Chromosome Location	chr6:27592003-27592004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27588632..27593657-chr6:27594318..27600598,11	K562	blood:
2	chr6:27585304..27588262-chr6:27590023..27594531,5	K562	blood:
3	chr6:27590776..27592562-chr6:27661680..27663552,2	MCF-7	breast:
4	chr6:27577554..27579986-chr6:27591493..27593783,2	K562	blood:
5	chr6:27585919..27588728-chr6:27591058..27593612,2	MCF-7	breast:
6	chr6:27591455..27593158-chr6:27596051..27599012,2	MCF-7	breast:
7	chr6:27591195..27593958-chr6:27774949..27777675,2	K562	blood:

Variant related genes	Relation type
ENSG00000196747	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000238648	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10484399	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13192965	1.00[EUR][1000 genomes]
rs13193480	0.94[EUR][1000 genomes]
rs13193542	0.94[EUR][1000 genomes]
rs13194781	0.83[EUR][1000 genomes]
rs13195636	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13195728	0.87[EUR][1000 genomes]
rs13202291	0.92[EUR][1000 genomes]
rs13202295	0.94[EUR][1000 genomes]
rs13202775	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13209332	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13210634	1.00[EUR][1000 genomes]
rs13212318	0.98[EUR][1000 genomes]
rs13212651	0.83[EUR][1000 genomes]
rs13215275	1.00[EUR][1000 genomes]
rs13217620	1.00[EUR][1000 genomes]
rs17749927	1.00[EUR][1000 genomes]
rs17750747	0.94[EUR][1000 genomes]
rs17751184	0.87[EUR][1000 genomes]
rs34064842	0.98[EUR][1000 genomes]
rs34105070	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34194357	0.83[EUR][1000 genomes]
rs34409918	0.98[EUR][1000 genomes]
rs34432857	0.98[EUR][1000 genomes]
rs34573979	0.81[EUR][1000 genomes]
rs34706883	0.87[EUR][1000 genomes]
rs34718920	0.87[EUR][1000 genomes]
rs34965299	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35037868	0.94[EUR][1000 genomes]
rs35501037	0.94[EUR][1000 genomes]
rs35819751	0.83[EUR][1000 genomes]
rs35848276	0.85[EUR][1000 genomes]
rs36116761	0.83[EUR][1000 genomes]
rs56405707	1.00[EUR][1000 genomes]
rs58616630	0.81[EUR][1000 genomes]
rs66785117	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67101035	0.87[EUR][1000 genomes]
rs67652222	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71559038	0.98[EUR][1000 genomes]
rs71559050	0.87[EUR][1000 genomes]
rs72845046	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72845070	1.00[EUR][1000 genomes]
rs72847313	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025572	chr6:27487852-27604454	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv538167	chr6:27487852-27604454	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv1018107	chr6:27503525-27596736	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv538168	chr6:27503525-27596736	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv1023673	chr6:27570731-27688782	Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35715914	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs35715914	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs35715914	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27586200-27592200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:27587800-27592200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:27591200-27592600	Enhancers	K562	blood
4	chr6:27591600-27592400	Enhancers	Duodenum Mucosa	Duodenum
5	chr6:27592000-27593200	Enhancers	Fetal Intestine Large	intestine

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