Variant report

Variant	rs62415933
Chromosome Location	chr6:57088776-57088777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:57088654..57090338-chr6:57110671..57112919,2	MCF-7	breast:
2	chr6:57085891..57087980-chr6:57088425..57091105,2	MCF-7	breast:
3	chr6:57085083..57088609-chr6:57088640..57091754,5	K562	blood:

Variant related genes	Relation type
ENSG00000112210	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1002996	0.83[AMR][1000 genomes]
rs1040461	0.83[AMR][1000 genomes]
rs1556245	0.83[AMR][1000 genomes]
rs16888316	0.83[AMR][1000 genomes]
rs2273919	0.83[AMR][1000 genomes]
rs3757296	0.83[AMR][1000 genomes]
rs58705880	0.83[AMR][1000 genomes]
rs61740375	0.83[AMR][1000 genomes]
rs62415861	0.83[AMR][1000 genomes]
rs62415863	0.83[AMR][1000 genomes]
rs62415864	0.83[AMR][1000 genomes]
rs62415878	0.83[AMR][1000 genomes]
rs62415879	0.83[AMR][1000 genomes]
rs62415880	0.83[AMR][1000 genomes]
rs62415885	0.83[AMR][1000 genomes]
rs62417430	0.83[AMR][1000 genomes]
rs6459179	0.83[AMR][1000 genomes]
rs72867038	0.83[AMR][1000 genomes]
rs72867054	0.90[AMR][1000 genomes]
rs72867059	0.90[AMR][1000 genomes]
rs72867062	0.90[AMR][1000 genomes]
rs7749960	0.81[AMR][1000 genomes]
rs7771328	0.83[AMR][1000 genomes]
rs9296860	0.83[AMR][1000 genomes]
rs9296861	0.83[AMR][1000 genomes]
rs9349845	0.81[AMR][1000 genomes]
rs9357939	0.90[AMR][1000 genomes]
rs9357940	0.83[AMR][1000 genomes]
rs9357941	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9367710	0.83[AMR][1000 genomes]
rs9367711	0.83[AMR][1000 genomes]
rs9367713	0.83[AMR][1000 genomes]
rs9370559	0.83[AMR][1000 genomes]
rs9370563	0.83[AMR][1000 genomes]
rs9370567	0.90[AMR][1000 genomes]
rs9370568	0.81[AMR][1000 genomes]
rs9382684	0.83[AMR][1000 genomes]
rs9382686	0.83[AMR][1000 genomes]
rs9382691	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9396255	0.83[AMR][1000 genomes]
rs9396261	0.83[AMR][1000 genomes]
rs9396263	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464418	0.83[AMR][1000 genomes]
rs9464419	0.83[AMR][1000 genomes]
rs9475782	0.83[AMR][1000 genomes]
rs9475783	0.83[AMR][1000 genomes]
rs9475788	0.83[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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv462949	chr6:56973902-57098973	ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv603190	chr6:56973902-57098973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57087600-57091400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:57087800-57089000	Weak transcription	Ovary	ovary
3	chr6:57087800-57089600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:57087800-57090200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:57087800-57090400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:57087800-57091000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:57088000-57089200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:57088000-57089200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:57088000-57089200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:57088000-57089200	Weak transcription	NHDF-Ad	bronchial
11	chr6:57088000-57089400	Weak transcription	A549	lung
12	chr6:57088000-57089600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:57088000-57090000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:57088000-57090800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:57088000-57091000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:57088000-57091000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:57088000-57091400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:57088000-57091600	Enhancers	Colon Smooth Muscle	Colon
19	chr6:57088200-57089000	Weak transcription	K562	blood
20	chr6:57088200-57089200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:57088200-57089200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:57088200-57089200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:57088200-57089200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:57088200-57089400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:57088200-57089400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:57088200-57089400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:57088200-57089400	Weak transcription	Osteobl	bone
28	chr6:57088200-57089600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:57088200-57089600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:57088200-57089600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:57088200-57089600	Weak transcription	Fetal Kidney	kidney
32	chr6:57088200-57089600	Weak transcription	Dnd41	blood
33	chr6:57088200-57089600	Weak transcription	NH-A	brain
34	chr6:57088200-57089800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:57088200-57091000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:57088200-57091000	Weak transcription	NHEK	skin
37	chr6:57088200-57091200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:57088200-57091400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:57088400-57088800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:57088600-57089600	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links