Variant report

Variant	rs12055809
Chromosome Location	chr6:128920211-128920212
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:128840068..128843152-chr6:128919180..128921740,3	MCF-7	breast:
2	chr6:128839123..128844576-chr6:128915695..128924187,20	MCF-7	breast:
3	chr6:128889715..128894242-chr6:128918492..128921414,6	MCF-7	breast:
4	chr6:128848533..128850915-chr6:128919226..128921374,2	MCF-7	breast:
5	chr6:128834237..128835841-chr6:128918392..128920731,2	MCF-7	breast:
6	chr6:128899252..128902077-chr6:128918932..128921970,3	MCF-7	breast:
7	chr6:128891192..128892170-chr6:128919419..128920258,2	MCF-7	breast:
8	chr6:128919408..128920317-chr6:129017818..129018321,2	MCF-7	breast:
9	chr6:128918449..128923023-chr6:128923258..128928829,7	MCF-7	breast:
10	chr6:128918845..128920868-chr6:128977642..128979259,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213130	Chromatin interaction
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1578518	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17056066	0.81[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.98[ASN][1000 genomes]
rs17056073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17056077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2092826	0.97[ASN][1000 genomes]
rs2326703	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4141680	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs59322395	0.82[ASN][1000 genomes]
rs6928257	0.97[ASN][1000 genomes]
rs6932252	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7451451	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs7765578	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9385467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9388656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9402058	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9482905	0.96[ASN][1000 genomes]
rs9492025	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv830801	chr6:128878436-129064667	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12055809	EPB41L2	cis	parietal	SCAN
rs12055809	C6orf174	cis	parietal	SCAN
rs12055809	RSPO3	cis	cerebellum	SCAN
rs12055809	SAMD3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128916000-128923400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:128916400-128922800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:128916600-128923200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:128916600-128923400	Enhancers	HMEC	breast
5	chr6:128917400-128921600	Weak transcription	Left Ventricle	heart
6	chr6:128917600-128921000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:128917600-128921400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:128917800-128920600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:128918200-128922400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:128918200-128922600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:128918400-128921200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:128918800-128920400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:128918800-128921400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:128918800-128921400	Enhancers	NH-A	brain
15	chr6:128918800-128922600	Enhancers	NHDF-Ad	bronchial
16	chr6:128919000-128922800	Enhancers	Fetal Heart	heart
17	chr6:128919400-128920400	Flanking Active TSS	NHEK	skin
18	chr6:128919400-128921200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:128919600-128923200	Enhancers	HSMM	muscle
20	chr6:128919800-128920400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:128919800-128921200	Enhancers	Stomach Mucosa	stomach
22	chr6:128920000-128921000	Enhancers	Osteobl	bone
23	chr6:128920000-128922400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:128920000-128923000	Enhancers	NHLF	lung
25	chr6:128920000-128928800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:128920200-128921000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr6:128920200-128921400	Enhancers	Pancreatic Islets	Pancreatic Islet

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