Variant report

Variant	rs56308612
Chromosome Location	chr6:28775667-28775668
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28774872..28779186-chr6:28780865..28786550,9	K562	blood:
2	chr6:28760359..28762539-chr6:28774291..28776179,2	K562	blood:
3	chr6:28768996..28771268-chr6:28774440..28778213,3	K562	blood:
4	chr6:28775179..28778043-chr6:28889400..28891921,3	MCF-7	breast:
5	chr6:28760359..28764219-chr6:28771578..28776179,5	K562	blood:
6	chr6:28774860..28778003-chr6:28805367..28807894,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM27-18	chr6:28773744-28776603	NONHSAT108486

No data

Variant related genes	Relation type
ENSG00000225173	Chromatin interaction
ENSG00000265764	Chromatin interaction
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10498733	0.81[AMR][1000 genomes]
rs169682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17280797	0.94[AMR][1000 genomes]
rs17280818	0.94[AMR][1000 genomes]
rs17281186	0.94[AMR][1000 genomes]
rs17346574	0.94[AMR][1000 genomes]
rs17375288	0.86[AFR][1000 genomes]
rs185982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1936180	0.81[AMR][1000 genomes]
rs209189	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs209190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209199	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2754761	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2754762	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2754765	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2765220	1.00[ASN][1000 genomes]
rs2765222	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765223	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3131344	1.00[ASN][1000 genomes]
rs3132372	1.00[ASN][1000 genomes]
rs398795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs417919	1.00[ASN][1000 genomes]
rs453020	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs55891766	0.94[AMR][1000 genomes]
rs56030816	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56110474	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs56374518	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56678427	0.92[AFR][1000 genomes]
rs57491524	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58104924	0.81[AMR][1000 genomes]
rs59959723	0.94[AMR][1000 genomes]
rs61094745	0.94[AMR][1000 genomes]
rs6938988	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6939948	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7755641	0.81[AMR][1000 genomes]
rs7760656	0.94[AMR][1000 genomes]
rs7765829	0.94[AMR][1000 genomes]
rs7766599	0.94[AMR][1000 genomes]
rs9257190	1.00[ASN][1000 genomes]
rs9257226	1.00[ASN][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	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883517	chr6:28751727-28802149	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv3384463	chr6:28759027-28776259	Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2621756	chr6:28762692-28779791	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv2322180	chr6:28764675-28780578	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv9558	chr6:28770281-28785058	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3410540	chr6:28770455-28785112	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3322630	chr6:28770519-28785092	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv3486939	chr6:28770525-28785051	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv3486940	chr6:28770525-28785051	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv3403106	chr6:28770790-28785189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28771400-28775800	Weak transcription	GM12878-XiMat	blood
2	chr6:28772800-28775800	Weak transcription	A549	lung
3	chr6:28775200-28778200	Weak transcription	Right Atrium	heart
4	chr6:28775600-28775800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:28775600-28775800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:28775600-28775800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:28775600-28775800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:28775600-28775800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:28775600-28775800	Bivalent/Poised TSS	HepG2	liver
10	chr6:28775600-28775800	Active TSS	Osteobl	bone
11	chr6:28775600-28776000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:28775600-28776000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
13	chr6:28775600-28776200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:28775600-28776200	Active TSS	NHEK	skin
15	chr6:28775600-28776400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:28775600-28776400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:28775600-28776400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:28775600-28776400	Bivalent/Poised TSS	HUVEC	blood vessel
19	chr6:28775600-28776400	Active TSS	NH-A	brain
20	chr6:28775600-28776400	Active TSS	NHLF	lung
21	chr6:28775600-28776600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr6:28775600-28776600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:28775600-28776600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:28775600-28776600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr6:28775600-28776600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr6:28775600-28776600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr6:28775600-28776600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:28775600-28776600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:28775600-28776600	Active TSS	K562	blood
30	chr6:28775600-28776800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
31	chr6:28775600-28776800	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:28775600-28776800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
33	chr6:28775600-28776800	Active TSS	Hela-S3	cervix
34	chr6:28775600-28777000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:28775600-28778600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr6:28775600-28778600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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