Variant report

Variant	rs3130275
Chromosome Location	chr6:33332137-33332138
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33331065..33333625-chr6:33356346..33358635,2	K562	blood:
2	chr6:33328288..33333241-chr6:33333249..33338819,6	K562	blood:
3	chr6:33329577..33332620-chr6:33339048..33342098,3	K562	blood:
4	chr6:33324046..33327931-chr6:33328359..33332196,5	K562	blood:

Variant related genes	Relation type
ENSG00000228285	Chromatin interaction
ENSG00000225644	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2136778	0.91[AFR][1000 genomes]
rs2743	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3117320	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130001	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130002	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130004	0.82[AMR][1000 genomes]
rs3130007	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3130015	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3130274	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130276	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs371005	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs376006	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs420714	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs442745	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs456993	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs459927	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs461887	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs461964	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs465223	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs465474	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs465506	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs465877	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs467065	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs583129	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9278025	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][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	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv970110	chr6:33331311-33342922	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3130275	TAPBP	Cis_1M	lymphoblastoid	RTeQTL
rs3130275	CDKN1A	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33322000-33332200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr6:33324400-33332600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:33324600-33340200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:33328200-33332200	Weak transcription	A549	lung
5	chr6:33330000-33332200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:33330600-33332200	Enhancers	K562	blood
7	chr6:33331000-33332200	Weak transcription	Hela-S3	cervix
8	chr6:33331400-33332600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:33331800-33332400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:33331800-33333200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:33331800-33333600	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr6:33332000-33332200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr6:33332000-33332200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr6:33332000-33332400	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr6:33332000-33332600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr6:33332000-33332800	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr6:33332000-33332800	Enhancers	Primary hematopoietic stem cells	blood
18	chr6:33332000-33333200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:33332000-33333200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:33332000-33333200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:33332000-33333600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links