Variant report

Variant	rs250253
Chromosome Location	chr5:106852966-106852967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs152554	0.99[EUR][1000 genomes]
rs153189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs250251	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388016	0.96[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs395561	1.00[CHD][hapmap];0.96[ASN][1000 genomes]
rs446774	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848827	0.96[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs848828	0.96[CEU][hapmap];0.96[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	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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	6 gene(s)	inside rSNPs	diseases
2	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs250253	SLC25A46	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106836400-106855800	Weak transcription	Aorta	Aorta
2	chr5:106838600-106855600	Weak transcription	Right Ventricle	heart
3	chr5:106839200-106855600	Weak transcription	HSMM	muscle
4	chr5:106842400-106880000	Weak transcription	Gastric	stomach
5	chr5:106845800-106855600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:106846000-106855800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:106847200-106853200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:106848200-106853200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:106848400-106855800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:106848800-106865000	Weak transcription	Right Atrium	heart
11	chr5:106849000-106855600	Weak transcription	Fetal Stomach	stomach
12	chr5:106849000-106859200	Weak transcription	Esophagus	oesophagus
13	chr5:106849200-106859000	Weak transcription	Left Ventricle	heart
14	chr5:106849800-106853200	Enhancers	GM12878-XiMat	blood
15	chr5:106849800-106854000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:106850000-106853400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:106850200-106854000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:106850200-106854400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:106850200-106855000	Weak transcription	Fetal Heart	heart
20	chr5:106850400-106853200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:106850400-106859000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:106850600-106854400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:106850600-106855200	Weak transcription	Fetal Kidney	kidney
24	chr5:106850600-106855400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:106850800-106853000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:106850800-106853200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:106850800-106853200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr5:106850800-106854000	Weak transcription	HMEC	breast
29	chr5:106850800-106855600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:106850800-106855600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:106850800-106855600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:106850800-106855600	Weak transcription	Thymus	Thymus
33	chr5:106850800-106855600	Weak transcription	NHEK	skin
34	chr5:106851000-106853400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr5:106851000-106855200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:106851000-106855200	Weak transcription	Fetal Thymus	thymus
37	chr5:106851400-106855600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:106852000-106855600	Weak transcription	NHDF-Ad	bronchial
39	chr5:106852000-106858200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr5:106852000-106859000	Weak transcription	Pancreas	Pancrea
41	chr5:106852400-106853000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr5:106852400-106853200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:106852600-106854000	Weak transcription	Dnd41	blood
44	chr5:106852600-106854200	Genic enhancers	A549	lung
45	chr5:106852600-106856600	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr5:106852800-106854200	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr5:106852800-106856400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:106852800-106856800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:106852800-106857400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:106852800-106860200	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links