Variant report

Variant	rs2629470
Chromosome Location	chr6:80176289-80176290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:80175533..80178362-chr6:80187176..80190126,2	K562	blood:
2	chr6:79784565..79790401-chr6:80174482..80177325,6	MCF-7	breast:
3	chr6:79789634..79791337-chr6:80176211..80178981,2	K562	blood:
4	chr6:79910795..79911579-chr6:80175671..80176696,3	MCF-7	breast:
5	chr6:80140948..80141831-chr6:80176082..80176626,3	MCF-7	breast:
6	chr6:79911023..79911795-chr6:80175584..80176322,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146247	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1394280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1485360	0.88[EUR][1000 genomes]
rs1485373	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1485374	0.84[CEU][hapmap]
rs2629471	0.91[CEU][hapmap];0.88[CHD][hapmap];0.86[EUR][1000 genomes]
rs2629474	0.91[CEU][hapmap]
rs2803181	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803182	0.93[EUR][1000 genomes];1.00[ASN][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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1030126	chr6:80113449-80209165	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv830707	chr6:80134625-80325171	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1029259	chr6:80142754-80340332	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv886303	chr6:80147225-80252423	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2629470	ME1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80171200-80220000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:80171600-80226600	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:80173200-80179600	Enhancers	HepG2	liver
4	chr6:80173600-80177200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:80173600-80177400	Weak transcription	Placenta	Placenta
6	chr6:80174000-80177600	Weak transcription	NHEK	skin
7	chr6:80174000-80191800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:80174200-80177400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:80174200-80177800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:80175200-80177800	Weak transcription	Pancreas	Pancrea
11	chr6:80175400-80177400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:80175400-80177400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:80175800-80178200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:80176000-80179000	Weak transcription	HUVEC	blood vessel
15	chr6:80176200-80176400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr6:80176200-80176400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:80176200-80176400	Enhancers	HMEC	breast
18	chr6:80176200-80176600	Enhancers	Adipose Nuclei	Adipose
19	chr6:80176200-80176800	Enhancers	K562	blood
20	chr6:80176200-80178400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:80176200-80179600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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