Variant report

Variant	rs25999
Chromosome Location	chr5:106805007-106805008
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:106803456..106805007-chr5:106904785..106907231,2	K562	blood:
2	chr5:106802607..106804706-chr5:106804946..106806862,2	MCF-7	breast:
3	chr5:106804269..106806001-chr5:106811560..106813893,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs25963	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs25995	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs25996	0.88[JPT][hapmap]
rs25998	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27445	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs27750	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs27853	0.88[JPT][hapmap]
rs27930	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv462379	chr5:106789764-106806438	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv471037	chr5:106789764-106806438	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv599334	chr5:106789764-106806438	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs25999	NUDT12	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106799400-106805800	Enhancers	HMEC	breast
2	chr5:106799400-106806400	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr5:106799600-106806200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:106799600-106806200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr5:106799600-106806200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr5:106799600-106806400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:106799600-106806400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr5:106799600-106806800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:106799600-106807000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:106799600-106807200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:106799600-106808200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr5:106799600-106811200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr5:106799600-106811800	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr5:106799800-106805200	Enhancers	Placenta Amnion	Placenta Amnion
15	chr5:106799800-106805200	Enhancers	NHEK	skin
16	chr5:106799800-106805600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:106799800-106806000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:106799800-106811000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:106800000-106806000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr5:106801600-106806400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:106802000-106805400	Enhancers	Fetal Heart	heart
22	chr5:106802400-106807000	Enhancers	Hela-S3	cervix
23	chr5:106802400-106810200	Weak transcription	Right Atrium	heart
24	chr5:106802600-106805200	Weak transcription	Fetal Kidney	kidney
25	chr5:106802600-106805200	Weak transcription	HSMMtube	muscle
26	chr5:106802600-106805200	Weak transcription	NHDF-Ad	bronchial
27	chr5:106802600-106805800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr5:106802600-106808200	Weak transcription	Gastric	stomach
29	chr5:106802600-106813600	Weak transcription	Right Ventricle	heart
30	chr5:106803200-106806200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:106803600-106806000	Enhancers	H1 Cell Line	embryonic stem cell
32	chr5:106803600-106808200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:106803600-106808400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:106803600-106812600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:106803800-106807000	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr5:106803800-106811400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr5:106804000-106805600	Enhancers	Muscle Satellite Cultured Cells	--
38	chr5:106804000-106805800	Enhancers	NH-A	brain
39	chr5:106804000-106806200	Enhancers	Dnd41	blood
40	chr5:106804000-106806200	Enhancers	HSMM	muscle
41	chr5:106804000-106806400	Enhancers	Stomach Mucosa	stomach
42	chr5:106804200-106806000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:106804200-106806000	Enhancers	Aorta	Aorta
44	chr5:106804200-106806000	Enhancers	Placenta	Placenta
45	chr5:106804200-106806400	Flanking Active TSS	A549	lung
46	chr5:106804200-106809800	Weak transcription	Fetal Intestine Small	intestine
47	chr5:106804400-106805200	Weak transcription	NHLF	lung
48	chr5:106804400-106806000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr5:106804400-106810200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr5:106804600-106805200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links