Variant report

Variant	rs6048962
Chromosome Location	chr20:23619359-23619360
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23617167..23619413-chr20:62495612..62498216,2	MCF-7	breast:
2	chr20:23400787..23402892-chr20:23617355..23620191,2	MCF-7	breast:
3	chr20:23608610..23615599-chr20:23616056..23619619,19	MCF-7	breast:
4	chr20:23342009..23344759-chr20:23616093..23619702,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125814	Chromatin interaction
ENSG00000270001	Chromatin interaction
ENSG00000125812	Chromatin interaction
ENSG00000101150	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs6036480	1.00[EUR][1000 genomes]
rs6048959	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv964381	chr20:23614805-23621846	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	esv3359195	chr20:23617352-23620750	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	esv3377051	chr20:23617777-23620325	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3336303	chr20:23617902-23620300	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23618600-23619400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:23618600-23619400	Enhancers	Small Intestine	intestine
3	chr20:23618600-23619400	Weak transcription	Spleen	Spleen
4	chr20:23618600-23619400	Weak transcription	HMEC	breast
5	chr20:23618600-23619600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr20:23618600-23620000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr20:23618600-23620000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr20:23618600-23620200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr20:23618600-23620400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr20:23618600-23620800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr20:23618600-23621000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr20:23618600-23621200	Weak transcription	Ovary	ovary
13	chr20:23618600-23621200	Weak transcription	GM12878-XiMat	blood
14	chr20:23618600-23621600	Weak transcription	Liver	Liver
15	chr20:23618600-23621600	Weak transcription	Brain Hippocampus Middle	brain
16	chr20:23618600-23621800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr20:23618600-23621800	Weak transcription	Left Ventricle	heart
18	chr20:23618600-23622000	Weak transcription	HUVEC	blood vessel
19	chr20:23618600-23622200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr20:23618600-23622400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr20:23618600-23622400	Weak transcription	NHDF-Ad	bronchial
22	chr20:23618600-23622400	Weak transcription	NHLF	lung
23	chr20:23618600-23622600	Weak transcription	Brain Anterior Caudate	brain
24	chr20:23618600-23622600	Weak transcription	Brain Substantia Nigra	brain
25	chr20:23618600-23622600	Weak transcription	Colon Smooth Muscle	Colon
26	chr20:23618600-23624800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr20:23618600-23626000	Weak transcription	Gastric	stomach
28	chr20:23618800-23619400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr20:23618800-23619400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr20:23618800-23619400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr20:23618800-23619400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr20:23618800-23619400	Weak transcription	Fetal Thymus	thymus
33	chr20:23618800-23619400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr20:23618800-23619400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr20:23618800-23619600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr20:23618800-23619600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr20:23618800-23619600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr20:23618800-23619600	Enhancers	Adipose Nuclei	Adipose
39	chr20:23618800-23619800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr20:23618800-23620000	Enhancers	NHEK	skin
41	chr20:23618800-23620400	Enhancers	A549	lung
42	chr20:23618800-23620600	Weak transcription	Fetal Intestine Large	intestine
43	chr20:23618800-23620800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr20:23618800-23621000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr20:23618800-23621200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr20:23618800-23621200	Weak transcription	Psoas Muscle	Psoas
47	chr20:23618800-23621400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr20:23618800-23621400	Weak transcription	Primary B cells from cord blood	blood
49	chr20:23618800-23621400	Weak transcription	HSMMtube	muscle
50	chr20:23618800-23621600	Weak transcription	Brain Cingulate Gyrus	brain

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