Variant report

Variant	rs9862131
Chromosome Location	chr3:48202440-48202441
allele	A/G
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	chr3:48202258-48202559	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:48202014-48202460	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48200857..48202800-chr3:48228103..48229714,2	MCF-7	breast:

Variant related genes	Relation type
SNRPFP4	TF binding region
ENSG00000164045	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 29 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11707606	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11709691	0.80[EUR][1000 genomes]
rs11710861	0.80[EUR][1000 genomes]
rs11715799	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11718329	0.80[EUR][1000 genomes]
rs11719365	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11928691	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13059037	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13068265	0.80[EUR][1000 genomes]
rs13087929	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13097450	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13099560	0.82[EUR][1000 genomes]
rs13100815	0.80[ASN][1000 genomes]
rs17786132	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2361685	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34513961	0.84[EUR][1000 genomes]
rs34728236	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35414021	0.80[ASN][1000 genomes]
rs35456569	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35942721	0.82[EUR][1000 genomes]
rs36020562	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36064160	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36092070	0.80[EUR][1000 genomes]
rs3729577	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731487	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731489	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731497	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731513	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731515	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731534	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731550	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731555	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131361	0.82[ASN][1000 genomes]
rs4131362	0.82[ASN][1000 genomes]
rs6442111	0.80[EUR][1000 genomes]
rs6775179	0.80[EUR][1000 genomes]
rs6791930	0.82[ASN][1000 genomes]
rs6794644	0.82[ASN][1000 genomes]
rs6796343	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs745116	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7636461	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7647817	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9311421	0.80[ASN][1000 genomes]
rs936426	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs936427	0.80[EUR][1000 genomes]
rs9830016	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9831531	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9834095	0.82[ASN][1000 genomes]
rs9847953	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9850672	0.80[EUR][1000 genomes]
rs9853804	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS 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 miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv1012024	chr3:48119229-48242670	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv834682	chr3:48138137-48311122	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:29)

SNP	Gene	Cis/trans	Tissue	Source
rs9862131	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs9862131	ZNF589	cis	Esophagus Mucosa	GTEx
rs9862131	MRPS18AP1	cis	Artery Aorta	GTEx
rs9862131	NME6	cis	Nerve Tibial	GTEx
rs9862131	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs9862131	MRPS18AP1	cis	Artery Tibial	GTEx
rs9862131	CDC25A	cis	Adipose Subcutaneous	GTEx
rs9862131	MRPS18AP1	cis	lung	GTEx
rs9862131	ZNF589	cis	Artery Aorta	GTEx
rs9862131	ZNF589	cis	Thyroid	GTEx
rs9862131	MRPS18AP1	cis	Nerve Tibial	GTEx
rs9862131	CDC25A	cis	Artery Tibial	GTEx
rs9862131	CDC25A	cis	Thyroid	GTEx
rs9862131	ZNF589	cis	Stomach	GTEx
rs9862131	ZNF589	cis	Artery Tibial	GTEx
rs9862131	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs9862131	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs9862131	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs9862131	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs9862131	MRPS18AP1	cis	Stomach	GTEx
rs9862131	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs9862131	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs9862131	NME6	cis	Esophagus Muscularis	GTEx
rs9862131	FCF1P2	cis	Artery Tibial	GTEx
rs9862131	NME6	cis	Muscle Skeletal	GTEx
rs9862131	ZNF589	cis	Nerve Tibial	GTEx
rs9862131	CDC25A	cis	Muscle Skeletal	GTEx
rs9862131	MRPS18AP1	cis	Thyroid	GTEx
rs9862131	ZNF589	cis	Esophagus Muscularis	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48193000-48205200	Weak transcription	Brain Anterior Caudate	brain
2	chr3:48193000-48205400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:48193000-48228400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:48193200-48205200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:48193200-48206800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:48193400-48206800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:48193400-48210400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:48193600-48202800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:48193600-48205200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:48193600-48228200	Weak transcription	Pancreas	Pancrea
11	chr3:48193800-48203000	Weak transcription	Colonic Mucosa	Colon
12	chr3:48193800-48205200	Weak transcription	Liver	Liver
13	chr3:48193800-48228400	Weak transcription	Adipose Nuclei	Adipose
14	chr3:48193800-48228600	Weak transcription	Brain Substantia Nigra	brain
15	chr3:48193800-48228800	Weak transcription	Brain Angular Gyrus	brain
16	chr3:48194000-48215600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:48194000-48217000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:48194000-48217600	Weak transcription	Right Atrium	heart
19	chr3:48194000-48228400	Weak transcription	Right Ventricle	heart
20	chr3:48194000-48228800	Weak transcription	Left Ventricle	heart
21	chr3:48194400-48206600	Weak transcription	Fetal Heart	heart
22	chr3:48195600-48226200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:48196800-48205600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:48196800-48211800	Weak transcription	Stomach Mucosa	stomach
25	chr3:48197600-48205200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:48197600-48211600	Strong transcription	Fetal Thymus	thymus
27	chr3:48197600-48227200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:48197800-48227600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:48198000-48212200	Strong transcription	Thymus	Thymus
30	chr3:48198400-48211800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:48198400-48220200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:48198400-48222000	Strong transcription	Dnd41	blood
33	chr3:48198400-48227600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:48198400-48227800	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr3:48198400-48228000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:48198400-48228000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:48198400-48228200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:48198400-48228200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:48198600-48211400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:48198800-48204400	Strong transcription	Fetal Lung	lung
41	chr3:48198800-48210000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:48198800-48212200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:48199000-48204200	Strong transcription	GM12878-XiMat	blood
44	chr3:48199000-48218600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:48199000-48227600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:48199200-48219400	Strong transcription	Fetal Stomach	stomach
47	chr3:48199200-48227800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:48199400-48204200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:48199400-48223000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:48199600-48204200	Strong transcription	HepG2	liver

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