Variant report

Variant	rs4141680
Chromosome Location	chr6:128921869-128921870
allele	C/T
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	chr6:128899252..128902077-chr6:128918932..128921970,3	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
ENSG00000213130	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];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1578518	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17056066	1.00[CHB][hapmap];1.00[JPT][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	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[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];1.00[JPT][hapmap]
rs7765578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs9402058	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]
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:45 , 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	chr6:128918200-128922400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:128918200-128922600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:128918800-128922600	Enhancers	NHDF-Ad	bronchial
8	chr6:128919000-128922800	Enhancers	Fetal Heart	heart
9	chr6:128919600-128923200	Enhancers	HSMM	muscle
10	chr6:128920000-128922400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:128920000-128923000	Enhancers	NHLF	lung
12	chr6:128920000-128928800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:128920400-128923400	Enhancers	Dnd41	blood
14	chr6:128920600-128922200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:128920600-128922600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:128920600-128922800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:128920800-128922600	Enhancers	HSMMtube	muscle
18	chr6:128921000-128922000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr6:128921000-128922400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr6:128921000-128922400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr6:128921000-128922400	Flanking Active TSS	Osteobl	bone
22	chr6:128921000-128922600	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr6:128921000-128922600	Enhancers	Fetal Lung	lung
24	chr6:128921000-128923400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:128921200-128922200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:128921200-128922200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:128921200-128922400	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr6:128921400-128922000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr6:128921400-128922200	Flanking Active TSS	NH-A	brain
30	chr6:128921600-128922000	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr6:128921600-128922000	Enhancers	Hela-S3	cervix
32	chr6:128921600-128922200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:128921600-128922200	Enhancers	Left Ventricle	heart
34	chr6:128921600-128922200	Enhancers	GM12878-XiMat	blood
35	chr6:128921600-128922400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:128921600-128922800	Enhancers	Fetal Thymus	thymus
37	chr6:128921600-128923200	Enhancers	Stomach Mucosa	stomach
38	chr6:128921800-128922000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr6:128921800-128922000	Flanking Active TSS	HUVEC	blood vessel
40	chr6:128921800-128922200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:128921800-128922200	Enhancers	Primary hematopoietic stem cells	blood
42	chr6:128921800-128922200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:128921800-128922200	Flanking Active TSS	NHEK	skin
44	chr6:128921800-128922400	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr6:128921800-128922600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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