Variant report

Variant	rs2056924
Chromosome Location	chr6:27690174-27690175
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: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	chr6:27100798..27103607-chr6:27688775..27690811,2	K562	blood:
3	chr6:27684698..27689044-chr6:27689656..27693289,4	K562	blood:
4	chr6:27687897..27691780-chr6:27691811..27694513,3	MCF-7	breast:
5	chr6:27665264..27666796-chr6:27688059..27690362,2	K562	blood:
6	chr6:27688928..27690631-chr6:27710497..27712546,2	MCF-7	breast:
7	chr6:27658926..27663446-chr6:27685398..27690588,6	K562	blood:
8	chr6:27659151..27662876-chr6:27687364..27691190,4	K562	blood:
9	chr6:27114795..27117088-chr6:27688794..27690487,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196787	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1022486	0.91[JPT][hapmap]
rs10946935	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs10946938	0.91[JPT][hapmap]
rs10946940	0.87[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs200480	0.81[JPT][hapmap]
rs2179096	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2294480	0.91[JPT][hapmap]
rs2294481	0.91[JPT][hapmap]
rs4713112	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs4713120	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57252182	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6456799	0.87[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs6915266	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs6915987	0.86[JPT][hapmap]
rs6916878	0.83[JPT][hapmap]
rs6921256	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs6934437	0.86[JPT][hapmap]
rs6934794	0.85[JPT][hapmap]
rs7764081	0.86[JPT][hapmap]
rs9295747	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9348772	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9366699	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9368527	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9380007	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9393830	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs9393831	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9468209	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9468213	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	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
6	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2056924	AL022393.7	cis	Muscle Skeletal	GTEx
rs2056924	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27681600-27692200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr6:27688600-27690200	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr6:27689400-27690200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:27689600-27690200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:27689600-27690400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
6	chr6:27689600-27691600	Weak transcription	NHEK	skin
7	chr6:27689600-27694200	Weak transcription	A549	lung
8	chr6:27689800-27690200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:27689800-27690200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:27689800-27690200	Enhancers	K562	blood
11	chr6:27690000-27690200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr6:27690000-27690200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
13	chr6:27690000-27690200	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:27690000-27690200	Enhancers	H9 Cell Line	embryonic stem cell
15	chr6:27690000-27690200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr6:27690000-27690200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
17	chr6:27690000-27690200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr6:27690000-27690200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:27690000-27690200	Enhancers	GM12878-XiMat	blood
20	chr6:27690000-27690200	Bivalent Enhancer	HepG2	liver

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