Variant report

Variant	rs57878280
Chromosome Location	chr6:119470164-119470165
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119450270..119451239-chr6:119468206..119470213,5	MCF-7	breast:
2	chr6:119256106..119257947-chr6:119468580..119471034,2	K562	blood:
3	chr6:119467858..119470789-chr6:119668770..119672252,3	K562	blood:
4	chr6:119214272..119216553-chr6:119469883..119471782,2	K562	blood:
5	chr6:119467902..119470326-chr6:119670828..119672747,2	MCF-7	breast:
6	chr6:119284318..119286217-chr6:119469822..119472613,2	K562	blood:

Variant related genes	Relation type
ENSG00000111879	Chromatin interaction
ENSG00000111877	Chromatin interaction
ENSG00000111885	Chromatin interaction
ENSG00000111875	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs57123834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58455165	1.00[EUR][1000 genomes]
rs59653792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59885310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60186711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6936120	1.00[EUR][1000 genomes]
rs7771134	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7775658	1.00[EUR][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	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv886570	chr6:119450888-119600556	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119457000-119474800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:119466200-119470200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:119466800-119470200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:119467600-119470200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:119467600-119470200	Enhancers	Hela-S3	cervix
6	chr6:119467800-119470200	Enhancers	Stomach Mucosa	stomach
7	chr6:119467800-119470600	Enhancers	NHLF	lung
8	chr6:119467800-119470800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr6:119467800-119470800	Enhancers	HMEC	breast
10	chr6:119468000-119470200	Enhancers	Left Ventricle	heart
11	chr6:119468000-119470200	Enhancers	HSMMtube	muscle
12	chr6:119468200-119470200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:119468600-119470200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:119468600-119470800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:119468800-119470200	Enhancers	Aorta	Aorta
16	chr6:119468800-119470200	Enhancers	Colon Smooth Muscle	Colon
17	chr6:119468800-119470200	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr6:119468800-119470400	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr6:119468800-119470600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:119468800-119470600	Flanking Active TSS	Osteobl	bone
21	chr6:119468800-119470800	Enhancers	Pancreas	Pancrea
22	chr6:119469000-119470600	Enhancers	HepG2	liver
23	chr6:119469000-119472200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:119469400-119470200	Enhancers	Right Ventricle	heart
25	chr6:119469400-119470400	Enhancers	Fetal Lung	lung
26	chr6:119469600-119470200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:119469600-119470200	Active TSS	Brain Anterior Caudate	brain
28	chr6:119469600-119470400	Flanking Active TSS	NHEK	skin
29	chr6:119469600-119470600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:119469600-119470600	Flanking Active TSS	NH-A	brain
31	chr6:119469600-119471000	Enhancers	K562	blood
32	chr6:119469800-119470200	Flanking Active TSS	Fetal Brain Male	brain
33	chr6:119469800-119470400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:119469800-119470400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:119469800-119470400	Active TSS	Brain Cingulate Gyrus	brain
36	chr6:119469800-119470400	Active TSS	Brain Hippocampus Middle	brain
37	chr6:119469800-119470400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:119469800-119470400	Active TSS	Fetal Brain Female	brain
39	chr6:119469800-119470800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr6:119469800-119472200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr6:119469800-119472200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:119469800-119476800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:119470000-119470200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:119470000-119470200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:119470000-119470200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
46	chr6:119470000-119470400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr6:119470000-119470400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr6:119470000-119470400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:119470000-119470400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:119470000-119470400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links