Variant report

Variant	rs9464161
Chromosome Location	chr6:54775385-54775386
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54711197..54712939-chr6:54774381..54776518,2	MCF-7	breast:
2	chr6:54712764..54715534-chr6:54774311..54776470,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs16886169	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16886182	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16886273	0.84[AFR][1000 genomes]
rs1948818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2143797	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57032855	0.88[AFR][1000 genomes]
rs58327945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59549804	0.88[AFR][1000 genomes]
rs7762739	0.82[YRI][hapmap]
rs9464162	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9464166	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs9475057	0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9475059	0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9475060	0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9475061	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9475062	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9475064	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9475067	0.92[AFR][1000 genomes]
rs9475072	0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs9475073	0.91[YRI][hapmap];0.92[AFR][1000 genomes]
rs9475075	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54765800-54780800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:54769000-54780800	Weak transcription	NHEK	skin
3	chr6:54770000-54781200	Weak transcription	HMEC	breast
4	chr6:54774600-54776600	Enhancers	Fetal Lung	lung
5	chr6:54774800-54781200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:54775000-54775400	Active TSS	Brain Angular Gyrus	brain
7	chr6:54775000-54775400	Active TSS	Brain Hippocampus Middle	brain
8	chr6:54775000-54775400	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr6:54775000-54775400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr6:54775000-54775400	Enhancers	Small Intestine	intestine
11	chr6:54775000-54775600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr6:54775000-54775600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:54775000-54775600	Active TSS	Brain Cingulate Gyrus	brain
14	chr6:54775000-54775600	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr6:54775000-54775800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr6:54775000-54775800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr6:54775000-54776000	Enhancers	Fetal Intestine Large	intestine
18	chr6:54775000-54776000	Enhancers	Fetal Intestine Small	intestine
19	chr6:54775200-54775400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:54775200-54775400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:54775200-54775400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:54775200-54775400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:54775200-54775400	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr6:54775200-54775600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:54775200-54775600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:54775200-54775600	Enhancers	Brain Anterior Caudate	brain
27	chr6:54775200-54775600	Enhancers	Brain Germinal Matrix	brain
28	chr6:54775200-54775600	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr6:54775200-54775600	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr6:54775200-54775600	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr6:54775200-54775600	Enhancers	Stomach Mucosa	stomach
32	chr6:54775200-54775800	Enhancers	Placenta Amnion	Placenta Amnion
33	chr6:54775200-54776000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:54775200-54776000	Enhancers	Fetal Brain Male	brain

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