Variant report

Variant	rs2424510
Chromosome Location	chr20:23043550-23043551
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23037834..23043617-chr20:23045683..23049258,6	MCF-7	breast:
2	chr20:23041795..23043675-chr20:23045042..23047650,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1040588	0.83[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1821119	0.92[EUR][1000 genomes]
rs1835702	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1835703	0.88[EUR][1000 genomes]
rs1835704	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1998079	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1998080	0.92[CEU][hapmap];0.92[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs2007743	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2019632	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2144939	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2207110	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2255937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424503	0.89[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2424509	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2424511	0.92[EUR][1000 genomes]
rs2567619	0.93[EUR][1000 genomes]
rs2749813	0.92[CEU][hapmap];0.90[GIH][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs2749817	0.93[EUR][1000 genomes]
rs6036291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048519	0.85[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs6048526	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048533	0.93[EUR][1000 genomes]
rs6076016	0.89[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6082997	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6083000	0.91[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	nsv912816	chr20:22757960-23062927	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2758516	chr20:23029404-23173240	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2758789	chr20:23029404-23179604	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2424510	THBD	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23038400-23046600	Enhancers	Fetal Lung	lung
2	chr20:23039800-23046000	Enhancers	Fetal Muscle Leg	muscle
3	chr20:23040200-23043600	Enhancers	Placenta	Placenta
4	chr20:23040200-23043800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr20:23040200-23043800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr20:23040200-23046800	Enhancers	Fetal Stomach	stomach
7	chr20:23040400-23043600	Enhancers	Left Ventricle	heart
8	chr20:23040400-23043600	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr20:23040400-23044400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr20:23040400-23044600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:23040400-23044800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr20:23040400-23044800	Enhancers	HUVEC	blood vessel
13	chr20:23040600-23043600	Enhancers	Ovary	ovary
14	chr20:23040600-23043600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr20:23040600-23044000	Enhancers	NHDF-Ad	bronchial
16	chr20:23040800-23044600	Enhancers	Fetal Kidney	kidney
17	chr20:23041200-23043600	Enhancers	NHLF	lung
18	chr20:23041600-23043600	Enhancers	K562	blood
19	chr20:23041600-23044000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr20:23041800-23043600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr20:23041800-23043600	Enhancers	NH-A	brain
22	chr20:23041800-23044200	Enhancers	Fetal Muscle Trunk	muscle
23	chr20:23042000-23043600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr20:23042000-23043800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr20:23042000-23043800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr20:23042000-23046000	Weak transcription	Stomach Mucosa	stomach
27	chr20:23042200-23043800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr20:23042200-23044000	Enhancers	H9 Cell Line	embryonic stem cell
29	chr20:23042200-23045200	Weak transcription	Small Intestine	intestine
30	chr20:23042200-23046200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr20:23042400-23043600	Enhancers	Stomach Smooth Muscle	stomach
32	chr20:23042400-23043800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr20:23042400-23043800	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr20:23042400-23044000	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr20:23042400-23044600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr20:23042600-23043600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr20:23042800-23043600	Enhancers	Lung	lung
38	chr20:23042800-23044800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr20:23043000-23043600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr20:23043000-23043600	Enhancers	Aorta	Aorta
41	chr20:23043000-23043600	Enhancers	Esophagus	oesophagus
42	chr20:23043000-23043600	Enhancers	Fetal Intestine Large	intestine
43	chr20:23043200-23043800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr20:23043200-23043800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr20:23043200-23043800	Enhancers	HSMM	muscle
46	chr20:23043200-23044200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr20:23043200-23045400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr20:23043200-23045600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr20:23043200-23046400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr20:23043400-23043600	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links