Variant report

Variant	rs60477577
Chromosome Location	chr6:13383655-13383656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13382356..13383974-chr6:13614219..13616340,2	MCF-7	breast:
2	chr6:13379880..13381834-chr6:13381972..13383883,2	MCF-7	breast:
3	chr6:13383245..13384081-chr6:13397182..13397976,2	MCF-7	breast:
4	chr6:13383495..13385578-chr6:13393149..13396280,3	K562	blood:
5	chr6:13379696..13382625-chr6:13383447..13385433,2	MCF-7	breast:
6	chr6:13381851..13383974-chr6:13486160..13487948,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187461	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000261071	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs508477	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55942054	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56119181	0.82[EUR][1000 genomes]
rs57991391	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458769	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903516	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926072	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821301	1.00[EUR][1000 genomes]
rs9463694	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13365800-13385400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:13366000-13386800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:13368400-13386600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:13376800-13386600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:13376800-13395200	Weak transcription	NHEK	skin
7	chr6:13377800-13395600	Weak transcription	Aorta	Aorta
8	chr6:13379200-13386600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:13380200-13389400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:13381000-13385800	Enhancers	Primary B cells from peripheral blood	blood
11	chr6:13381200-13384000	Weak transcription	Right Ventricle	heart
12	chr6:13381800-13383800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:13381800-13384600	Enhancers	Primary B cells from cord blood	blood
14	chr6:13381800-13395400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:13382000-13383800	Weak transcription	Colonic Mucosa	Colon
16	chr6:13382000-13383800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr6:13382000-13385200	Weak transcription	K562	blood
18	chr6:13382000-13386600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:13382200-13384200	Weak transcription	Left Ventricle	heart
20	chr6:13382200-13384800	Weak transcription	Right Atrium	heart
21	chr6:13382400-13386600	Weak transcription	Lung	lung
22	chr6:13382400-13397600	Weak transcription	Esophagus	oesophagus
23	chr6:13382800-13384600	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr6:13382800-13385600	Enhancers	Liver	Liver
25	chr6:13383200-13384200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:13383200-13384200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr6:13383200-13384600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr6:13383400-13383800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr6:13383400-13383800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:13383400-13383800	Enhancers	Brain Anterior Caudate	brain
31	chr6:13383400-13383800	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr6:13383400-13384000	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr6:13383400-13384000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr6:13383400-13384000	Enhancers	Brain Substantia Nigra	brain
35	chr6:13383400-13384000	Enhancers	Fetal Lung	lung
36	chr6:13383400-13384000	Enhancers	Psoas Muscle	Psoas
37	chr6:13383400-13384000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr6:13383400-13384200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:13383400-13384200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:13383400-13384200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:13383400-13384200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:13383400-13384200	Enhancers	Adipose Nuclei	Adipose
43	chr6:13383400-13384200	Enhancers	A549	lung
44	chr6:13383400-13384400	Enhancers	Stomach Smooth Muscle	stomach
45	chr6:13383400-13384800	Enhancers	Colon Smooth Muscle	Colon
46	chr6:13383400-13385000	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr6:13383400-13385600	Enhancers	Primary T cells fromperipheralblood	blood
48	chr6:13383400-13385800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:13383400-13385800	Enhancers	Fetal Heart	heart
50	chr6:13383400-13386000	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links