Variant report

Variant	rs9402058
Chromosome Location	chr6:128922744-128922745
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:128839123..128844576-chr6:128915695..128924187,20	MCF-7	breast:
2	chr6:128840245..128843043-chr6:128922108..128924304,2	MCF-7	breast:
3	chr6:128918449..128923023-chr6:128923258..128928829,7	MCF-7	breast:
4	chr6:128916770..128918445-chr6:128921610..128924468,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12055809	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1578518	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17056066	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17056073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17056077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092826	0.96[ASN][1000 genomes]
rs2326703	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4141680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59322395	0.82[ASN][1000 genomes]
rs6928257	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6932252	0.95[ASN][1000 genomes]
rs7451451	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs7765578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9388656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9482905	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9492025	0.95[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

No data

Chromatin state (count:28 , 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	chr6:128919000-128922800	Enhancers	Fetal Heart	heart
6	chr6:128919600-128923200	Enhancers	HSMM	muscle
7	chr6:128920000-128923000	Enhancers	NHLF	lung
8	chr6:128920000-128928800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:128920400-128923400	Enhancers	Dnd41	blood
10	chr6:128920600-128922800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:128921000-128923400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:128921600-128922800	Enhancers	Fetal Thymus	thymus
13	chr6:128921600-128923200	Enhancers	Stomach Mucosa	stomach
14	chr6:128922000-128922800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr6:128922000-128923000	Enhancers	HUVEC	blood vessel
16	chr6:128922000-128923200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:128922200-128922800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:128922200-128922800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:128922200-128923400	Enhancers	NHEK	skin
20	chr6:128922200-128924000	Weak transcription	Left Ventricle	heart
21	chr6:128922200-128927000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:128922400-128922800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr6:128922400-128922800	Enhancers	Osteobl	bone
24	chr6:128922400-128923000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:128922400-128927000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:128922600-128923600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:128922600-128926800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:128922600-128927200	Weak transcription	NHDF-Ad	bronchial

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