Variant report

Variant	rs3113490
Chromosome Location	chr4:129965671-129965672
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11934740	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13109003	0.87[AMR][1000 genomes]
rs1374491	0.87[AMR][1000 genomes]
rs1699379	0.88[AMR][1000 genomes]
rs1699384	0.84[AMR][1000 genomes]
rs1699385	0.88[AMR][1000 genomes]
rs1699388	0.80[YRI][hapmap];0.88[AMR][1000 genomes]
rs1699389	0.88[AMR][1000 genomes]
rs1699391	0.80[YRI][hapmap];0.88[AMR][1000 genomes]
rs1699393	0.84[AMR][1000 genomes]
rs1699394	0.84[AMR][1000 genomes]
rs17185550	0.82[YRI][hapmap]
rs172168	0.80[JPT][hapmap]
rs1756012	0.85[AMR][1000 genomes]
rs1757930	0.84[AMR][1000 genomes]
rs1757936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1757938	0.80[JPT][hapmap]
rs1854773	0.85[AMR][1000 genomes]
rs2592948	0.80[JPT][hapmap]
rs280594	0.93[YRI][hapmap];0.94[AFR][1000 genomes]
rs280595	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28711799	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099899	0.80[YRI][hapmap]
rs3113487	0.80[JPT][hapmap]
rs3113489	0.85[AMR][1000 genomes]
rs337263	0.80[AMR][1000 genomes]
rs337275	0.83[AMR][1000 genomes]
rs389376	0.83[AMR][1000 genomes]
rs391396	0.83[AMR][1000 genomes]
rs395864	0.83[AMR][1000 genomes]
rs487233	0.83[AMR][1000 genomes]
rs487501	0.83[AMR][1000 genomes]
rs4975193	0.81[YRI][hapmap];0.88[AMR][1000 genomes]
rs4975194	0.88[AMR][1000 genomes]
rs517659	0.83[AMR][1000 genomes]
rs58689608	0.88[AMR][1000 genomes]
rs6534707	0.85[AMR][1000 genomes]
rs6812361	0.83[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6824219	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7671508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs789982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv522694	chr4:129862073-129994690	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3113490	C4orf33	cis	Artery Tibial	GTEx
rs3113490	C4orf33	cis	multi-tissue	Pritchard
rs3113490	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs3113490	LOC132321	cis	normal skin	skin_eQTL
rs3113490	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs3113490	C4orf33	cis	Lymphoblastoid	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129945600-129981800	Weak transcription	Thymus	Thymus
2	chr4:129951200-129967200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:129951400-129976200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:129958800-129966400	Weak transcription	Fetal Thymus	thymus
5	chr4:129959800-129966000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:129961400-129967800	Weak transcription	HSMM	muscle
7	chr4:129964400-129966400	Weak transcription	Monocytes-CD14+_RO01746	blood

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