Variant report

Variant	rs62250900
Chromosome Location	chr3:53829404-53829405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr3:53829292-53829542	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:53829269-53829568	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr3:53829211-53829567	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr3:53829368-53829457	MCF10A-Er-Src	breast:	n/a	chr3:53829408-53829419
5	STAT3	chr3:53829365-53829524	MCF10A-Er-Src	breast:	n/a	chr3:53829408-53829419

Variant related genes	Relation type
CACNA1D	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs13062035	1.00[ASN][1000 genomes]
rs13086947	1.00[ASN][1000 genomes]
rs14165	1.00[ASN][1000 genomes]
rs2289211	0.81[EUR][1000 genomes]
rs34565662	1.00[ASN][1000 genomes]
rs34723699	1.00[ASN][1000 genomes]
rs36006337	1.00[ASN][1000 genomes]
rs36077841	1.00[ASN][1000 genomes]
rs3774601	0.92[EUR][1000 genomes]
rs3774604	0.87[EUR][1000 genomes]
rs3774605	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687586	1.00[ASN][1000 genomes]
rs4687587	1.00[ASN][1000 genomes]
rs6445606	1.00[ASN][1000 genomes]
rs71301848	1.00[ASN][1000 genomes]
rs893362	1.00[ASN][1000 genomes]
rs920252	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1003204	chr3:53820070-53877149	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1002375	chr3:53822319-53872753	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53807600-53829800	Weak transcription	Brain Angular Gyrus	brain
2	chr3:53808800-53830200	Weak transcription	Pancreas	Pancrea
3	chr3:53811400-53838600	Weak transcription	Spleen	Spleen
4	chr3:53811600-53843600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:53815400-53829800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:53819600-53830000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:53822800-53832000	Weak transcription	Fetal Lung	lung
8	chr3:53823800-53832200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:53824400-53832000	Weak transcription	Fetal Intestine Large	intestine
10	chr3:53827200-53830200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:53827800-53832200	Weak transcription	Fetal Intestine Small	intestine
12	chr3:53828000-53830400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:53828200-53829800	Enhancers	NHDF-Ad	bronchial
14	chr3:53828200-53830200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:53828200-53830400	Enhancers	HMEC	breast
16	chr3:53828200-53830600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:53828200-53830600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:53828200-53830600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:53828400-53829600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:53828400-53830400	Enhancers	NHEK	skin
21	chr3:53828800-53830600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:53828800-53830600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:53828800-53830600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:53829200-53830000	Weak transcription	Brain Anterior Caudate	brain
25	chr3:53829200-53833800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:53829200-53853000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:53829400-53829800	Weak transcription	Esophagus	oesophagus
28	chr3:53829400-53830600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:53829400-53830800	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links