Variant report

Variant	rs34064842
Chromosome Location	chr6:27688625-27688626
allele	G/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27686786..27690624-chr6:27717358..27721129,5	K562	blood:
2	chr6:27683083..27685640-chr6:27686917..27688772,2	MCF-7	breast:
3	chr6:27687163..27689366-chr6:27693364..27696456,4	K562	blood:
4	chr6:27687897..27691780-chr6:27691811..27694513,3	MCF-7	breast:
5	chr6:27665264..27666796-chr6:27688059..27690362,2	K562	blood:
6	chr6:27660493..27662208-chr6:27687324..27689056,2	MCF-7	breast:
7	chr6:27658926..27663446-chr6:27685398..27690588,6	K562	blood:
8	chr6:27684698..27689044-chr6:27689656..27693289,4	K562	blood:
9	chr6:27659151..27662876-chr6:27687364..27691190,4	K562	blood:

No data

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10484399	0.85[EUR][1000 genomes]
rs13192965	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13193480	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13193542	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13194781	0.85[EUR][1000 genomes]
rs13195636	0.83[EUR][1000 genomes]
rs13195728	0.89[EUR][1000 genomes]
rs13199649	0.84[EUR][1000 genomes]
rs13199772	0.85[EUR][1000 genomes]
rs13199906	0.85[EUR][1000 genomes]
rs13202291	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13202295	0.96[EUR][1000 genomes]
rs13202775	0.91[EUR][1000 genomes]
rs13209332	0.83[EUR][1000 genomes]
rs13210634	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13212318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13212651	0.85[EUR][1000 genomes]
rs13215275	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13217620	0.98[EUR][1000 genomes]
rs17695758	0.85[EUR][1000 genomes]
rs17749927	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17750747	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17751184	0.89[EUR][1000 genomes]
rs17763089	0.85[EUR][1000 genomes]
rs34105070	0.91[EUR][1000 genomes]
rs34194357	0.85[EUR][1000 genomes]
rs34409918	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34432857	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34706883	0.89[EUR][1000 genomes]
rs34718920	0.89[EUR][1000 genomes]
rs34788973	0.82[EUR][1000 genomes]
rs34965299	0.83[EUR][1000 genomes]
rs35037868	0.96[EUR][1000 genomes]
rs35501037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35715914	0.98[EUR][1000 genomes]
rs35819751	0.85[EUR][1000 genomes]
rs35848276	0.83[EUR][1000 genomes]
rs36116761	0.85[EUR][1000 genomes]
rs45509595	0.85[EUR][1000 genomes]
rs56405707	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61742093	0.82[EUR][1000 genomes]
rs66785117	0.83[EUR][1000 genomes]
rs66868086	0.85[EUR][1000 genomes]
rs67040724	0.82[EUR][1000 genomes]
rs67101035	0.89[EUR][1000 genomes]
rs67652222	0.96[EUR][1000 genomes]
rs71559038	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71559050	0.89[EUR][1000 genomes]
rs71559054	0.82[EUR][1000 genomes]
rs72845046	0.96[EUR][1000 genomes]
rs72845070	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72847313	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
5	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv601204	chr6:27655564-27689502	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	esv3327708	chr6:27683503-27692934	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34064842	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs34064842	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs34064842	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27662800-27689000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:27678800-27689000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:27681200-27688800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:27681200-27688800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:27681600-27692200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:27687800-27689800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:27688400-27689000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:27688400-27689200	Enhancers	HMEC	breast
9	chr6:27688400-27689600	Flanking Active TSS	NHEK	skin
10	chr6:27688600-27688800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
11	chr6:27688600-27688800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr6:27688600-27688800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:27688600-27688800	Flanking Active TSS	A549	lung
14	chr6:27688600-27688800	Flanking Active TSS	K562	blood
15	chr6:27688600-27689400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr6:27688600-27689400	Flanking Active TSS	HepG2	liver
17	chr6:27688600-27689600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:27688600-27689600	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr6:27688600-27689600	Flanking Active TSS	GM12878-XiMat	blood
20	chr6:27688600-27689800	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr6:27688600-27689800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:27688600-27690000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr6:27688600-27690000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:27688600-27690000	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr6:27688600-27690000	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr6:27688600-27690000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:27688600-27690200	Active TSS	iPS-18 Cell Line	embryonic stem cell

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