Variant report

Variant	rs4481150
Chromosome Location	chr3:52837793-52837794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52836954..52839305-chr3:52853241..52854782,2	K562	blood:
2	chr3:52818249..52820505-chr3:52837668..52840542,3	K562	blood:
3	chr3:52831402..52833454-chr3:52836536..52839409,2	K562	blood:
4	chr3:52831117..52833454-chr3:52835406..52839409,3	K562	blood:
5	chr3:52827519..52829330-chr3:52834424..52837850,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000055955	Chromatin interaction
ENSG00000055957	Chromatin interaction
ENSG00000162267	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1042779	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1075653	0.81[JPT][hapmap]
rs1076425	0.81[JPT][hapmap]
rs13082960	0.80[CHB][hapmap]
rs2019065	0.81[CHB][hapmap]
rs2071044	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2071506	0.81[JPT][hapmap]
rs2071508	0.81[JPT][hapmap]
rs2239549	0.81[JPT][hapmap]
rs2239551	0.81[JPT][hapmap]
rs2268023	0.81[JPT][hapmap]
rs2270197	0.81[JPT][hapmap]
rs2300149	0.81[JPT][hapmap]
rs2302417	0.86[EUR][1000 genomes]
rs2535627	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.84[MKK][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2535629	0.81[CHB][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2710323	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3617	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3774354	0.81[JPT][hapmap]
rs4687550	0.81[JPT][hapmap]
rs736408	0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9324	0.81[JPT][hapmap]
rs9881468	0.81[JPT][hapmap]

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	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1010761	chr3:52804547-52851258	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4481150	ITIH4	cis	Lymphoblastoid	GTEx
rs4481150	FLJ12442	cis	multi-tissue	Pritchard
rs4481150	ITIH4	cis	multi-tissue	Pritchard
rs4481150	NT5DC2	cis	multi-tissue	Pritchard
rs4481150	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52834000-52838000	Weak transcription	Fetal Thymus	thymus
2	chr3:52834000-52841600	Strong transcription	HepG2	liver
3	chr3:52834200-52839800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:52835000-52843800	Strong transcription	Liver	Liver
5	chr3:52836800-52838000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:52836800-52851600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:52836800-52851800	Weak transcription	Pancreas	Pancrea
8	chr3:52837200-52839800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:52837200-52841400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:52837600-52838000	Genic enhancers	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links