Variant report

Variant	rs2740541
Chromosome Location	chr13:50914855-50914856
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50910484..50912390-chr13:50913694..50915729,2	MCF-7	breast:
2	chr13:50907927..50911991-chr13:50914729..50916836,3	K562	blood:
3	chr13:50902731..50904245-chr13:50913410..50915488,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176124	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1262865	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1326125	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2109236	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2159440	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2532966	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2532973	0.84[ASN][1000 genomes]
rs2532977	0.81[ASN][1000 genomes]
rs2580182	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2740531	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2762055	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2762057	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2762059	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2762064	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2812221	0.84[ASN][1000 genomes]
rs3990215	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50909200-50918600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr13:50909400-50915200	Weak transcription	Fetal Kidney	kidney
3	chr13:50909800-50915200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:50911400-50915400	Weak transcription	Aorta	Aorta
5	chr13:50912600-50916000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr13:50912800-50915000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr13:50912800-50915000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:50913000-50916400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr13:50913000-50921000	Weak transcription	HepG2	liver
10	chr13:50913400-50915000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr13:50913600-50915800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr13:50913800-50916000	Enhancers	Fetal Muscle Leg	muscle
13	chr13:50914000-50915200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr13:50914000-50915200	Enhancers	Fetal Muscle Trunk	muscle
15	chr13:50914000-50915600	Enhancers	Adipose Nuclei	Adipose
16	chr13:50914200-50915000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr13:50914200-50915200	Enhancers	Fetal Heart	heart
18	chr13:50914400-50915400	Enhancers	Brain Germinal Matrix	brain
19	chr13:50914400-50915400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr13:50914600-50915000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr13:50914600-50915000	Active TSS	Brain Anterior Caudate	brain
22	chr13:50914600-50915000	Active TSS	Brain Cingulate Gyrus	brain
23	chr13:50914600-50915000	Active TSS	Brain Hippocampus Middle	brain
24	chr13:50914600-50915200	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr13:50914600-50915400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr13:50914600-50915600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr13:50914600-50915600	ZNF genes & repeats	Fetal Thymus	thymus
28	chr13:50914600-50915800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr13:50914800-50915000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:50914800-50915000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr13:50914800-50915000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr13:50914800-50915000	Enhancers	Brain Angular Gyrus	brain
33	chr13:50914800-50915000	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr13:50914800-50915400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr13:50914800-50915600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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