Variant report

Variant	rs8177240
Chromosome Location	chr3:133477701-133477702
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:133470213-133490385	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:133471573-133479086	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:133477393-133478670	HepG2	liver:	n/a	n/a
4	MBD4	chr3:133477652-133478030	HepG2	liver:	n/a	n/a
5	HEY1	chr3:133470261-133482084	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:133471516-133487597	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:133464423-133479250	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:133476761-133478522	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:133470633-133487808	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133475218..133478981-chr3:133481312..133484055,3	K562	blood:

Variant related genes	Relation type
ENSG00000244062	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11710936	0.82[CHB][hapmap]
rs12490148	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs12595	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1358024	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs1525889	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1534165	0.82[CHB][hapmap]
rs2293375	0.85[CHB][hapmap]
rs34252038	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34805309	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811647	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811658	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854760	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4854761	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4854762	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6439439	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762719	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794945	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs7638018	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8177245	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177247	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8177252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177256	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177259	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177260	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177261	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177262	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177271	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8177272	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177295	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9843728	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[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	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv877508	chr3:133476852-133482662	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

Variant related diseases (count:3)

Disease	PMID	Source
Iron status biomarkers (transferrin levels)	25352340	GWAS catalog
Iron status biomarkers (iron levels)	25352340	GWAS catalog
Iron status biomarkers (transferrin saturation)	25352340	GWAS catalog

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133465600-133483000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:133472400-133480600	Strong transcription	Brain Angular Gyrus	brain
3	chr3:133473400-133480800	Strong transcription	Brain Inferior Temporal Lobe	brain
4	chr3:133473800-133478200	Strong transcription	Liver	Liver
5	chr3:133474000-133480200	Strong transcription	Brain Hippocampus Middle	brain
6	chr3:133475000-133487000	Weak transcription	Fetal Brain Male	brain
7	chr3:133475200-133480800	Strong transcription	HepG2	liver
8	chr3:133475200-133482800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:133476200-133477800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:133476200-133478600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:133476400-133478400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr3:133476800-133478200	Strong transcription	Brain Substantia Nigra	brain
13	chr3:133476800-133478800	Strong transcription	Adipose Nuclei	Adipose
14	chr3:133477000-133478000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:133477000-133478800	Strong transcription	Brain Cingulate Gyrus	brain
16	chr3:133477000-133490400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:133477200-133478400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr3:133477200-133480400	Strong transcription	Brain Anterior Caudate	brain
19	chr3:133477600-133478200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links