Variant report

Variant	rs4712046
Chromosome Location	chr6:53663316-53663317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53652474..53654178-chr6:53661361..53663423,2	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs56044016	1.00[AMR][1000 genomes]
rs6933533	1.00[AMR][1000 genomes]
rs73432412	1.00[AMR][1000 genomes]
rs73432448	1.00[AMR][1000 genomes]
rs73445791	1.00[AMR][1000 genomes]
rs7770003	1.00[AMR][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv3474747	chr6:53648744-53677210	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3474748	chr6:53648758-53677207	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53663600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:53661400-53666400	Weak transcription	Primary B cells from cord blood	blood
3	chr6:53661400-53666600	Weak transcription	Aorta	Aorta
4	chr6:53661400-53667200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:53661400-53668000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:53661400-53668000	Weak transcription	Ovary	ovary
7	chr6:53661400-53669800	Weak transcription	Gastric	stomach
8	chr6:53661400-53670400	Weak transcription	Primary T cells from cord blood	blood
9	chr6:53661400-53675600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
11	chr6:53661600-53663600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:53661600-53663600	Weak transcription	Colonic Mucosa	Colon
13	chr6:53661600-53664000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:53661600-53665000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:53661600-53665800	Weak transcription	NHLF	lung
16	chr6:53661800-53664000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:53662000-53670200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:53662200-53665800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:53662200-53667200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:53662400-53663600	Weak transcription	HUVEC	blood vessel
21	chr6:53662400-53664000	Weak transcription	Colon Smooth Muscle	Colon
22	chr6:53662400-53664200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr6:53662400-53664600	Weak transcription	Brain Substantia Nigra	brain
24	chr6:53662400-53667400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:53662400-53668000	Weak transcription	NH-A	brain
26	chr6:53662600-53663600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:53662600-53663800	Weak transcription	Placenta	Placenta
28	chr6:53662600-53664000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:53662600-53664200	Weak transcription	Hela-S3	cervix
30	chr6:53662600-53664800	Enhancers	HepG2	liver
31	chr6:53662600-53665800	Weak transcription	Brain Anterior Caudate	brain
32	chr6:53662600-53666800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:53662600-53666800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:53662600-53668000	Weak transcription	Pancreas	Pancrea
35	chr6:53662600-53669600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:53662600-53670000	Weak transcription	Esophagus	oesophagus
37	chr6:53662600-53670400	Weak transcription	Thymus	Thymus
38	chr6:53662600-53677600	Weak transcription	Small Intestine	intestine
39	chr6:53662800-53663600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr6:53662800-53667800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:53662800-53668000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr6:53662800-53668000	Weak transcription	NHEK	skin
43	chr6:53662800-53669800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:53662800-53669800	Weak transcription	HMEC	breast
45	chr6:53662800-53670200	Weak transcription	Fetal Intestine Large	intestine
46	chr6:53662800-53670200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr6:53662800-53675400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr6:53663000-53663400	Weak transcription	Fetal Thymus	thymus
49	chr6:53663000-53663600	Enhancers	Dnd41	blood
50	chr6:53663000-53664000	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links