Variant report

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10510773	0.81[CHD][hapmap]
rs12490327	0.88[CHD][hapmap]
rs12496821	0.88[CHD][hapmap]
rs12497334	0.83[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13060843	0.80[AMR][1000 genomes]
rs13068008	0.87[CHD][hapmap]
rs13086256	0.88[CHD][hapmap]
rs13095178	0.88[CHD][hapmap]
rs13096365	0.80[AMR][1000 genomes]
rs1344671	0.82[CHD][hapmap]
rs1520575	0.88[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes]
rs17815840	0.88[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes]
rs1882322	0.82[CHD][hapmap]
rs1921548	0.82[CHD][hapmap]
rs2359861	0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs34592432	0.85[AMR][1000 genomes]
rs34836904	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36021053	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3864001	0.88[CHD][hapmap]
rs3906509	0.88[CHD][hapmap]
rs4083342	0.88[CHD][hapmap]
rs4541376	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs500382	0.81[AMR][1000 genomes]
rs573279	0.80[MEX][hapmap]
rs71301895	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623961	0.88[CHD][hapmap]
rs7636321	0.82[CHD][hapmap]

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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13084347	NISCH	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54651000-54666400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:54652800-54665000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:54654000-54667000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:54655600-54662800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:54658800-54662800	Weak transcription	Ovary	ovary
6	chr3:54659200-54664600	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:54659800-54662800	Weak transcription	Brain Anterior Caudate	brain
8	chr3:54659800-54664400	Weak transcription	Spleen	Spleen
9	chr3:54660400-54663000	Weak transcription	Esophagus	oesophagus
10	chr3:54660400-54666800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:54662200-54662600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:54662400-54662600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr3:54662400-54663000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:54662400-54663600	Strong transcription	Stomach Smooth Muscle	stomach
15	chr3:54662400-54664600	Enhancers	HMEC	breast
16	chr3:54662400-54665200	Strong transcription	Right Atrium	heart

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