Variant report

Variant	rs9844531
Chromosome Location	chr3:53171822-53171823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53171302..53172940-chr3:53173107..53174967,2	K562	blood:
2	chr3:53171440..53173216-chr3:53176278..53178041,2	K562	blood:
3	chr3:53162508..53166145-chr3:53169616..53173018,3	K562	blood:

Variant related genes	Relation type
ENSG00000163933	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11130341	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12630819	0.85[EUR][1000 genomes]
rs12638996	0.84[EUR][1000 genomes]
rs13319872	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13433700	0.84[EUR][1000 genomes]
rs1560332	0.95[EUR][1000 genomes]
rs2564944	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28501212	0.86[EUR][1000 genomes]
rs28734933	0.86[EUR][1000 genomes]
rs3796351	0.83[EUR][1000 genomes]
rs4282053	0.83[EUR][1000 genomes]
rs4687570	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57261253	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57514626	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61296683	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445565	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6445566	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6769931	0.85[EUR][1000 genomes]
rs6769944	0.85[EUR][1000 genomes]
rs6777975	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6783748	0.85[EUR][1000 genomes]
rs6784207	0.96[EUR][1000 genomes]
rs6792345	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6792363	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6799837	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6809973	0.85[EUR][1000 genomes]
rs73088322	0.83[EUR][1000 genomes]
rs73088327	0.83[EUR][1000 genomes]
rs73088342	0.85[EUR][1000 genomes]
rs9757079	0.86[EUR][1000 genomes]
rs9817467	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9820125	0.86[EUR][1000 genomes]
rs9820324	0.86[EUR][1000 genomes]
rs9824325	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9828221	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9830353	0.87[EUR][1000 genomes]
rs9834111	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9845021	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9845352	0.81[EUR][1000 genomes]
rs9845484	0.82[EUR][1000 genomes]
rs9858469	0.86[EUR][1000 genomes]
rs9861744	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9867023	0.85[EUR][1000 genomes]
rs9867590	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9868263	0.88[EUR][1000 genomes]
rs9868406	0.87[EUR][1000 genomes]
rs9872260	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9878875	0.85[EUR][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	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv3381848	chr3:53167712-53172310	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9844531	RFT1	cis	Esophagus Muscularis	GTEx
rs9844531	SERBP1P3	cis	Thyroid	GTEx
rs9844531	RFT1	cis	Artery Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53165000-53176200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:53165000-53176400	Weak transcription	Aorta	Aorta
3	chr3:53165400-53173800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:53165400-53176000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:53165600-53173400	Weak transcription	Gastric	stomach
6	chr3:53165600-53174200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:53165600-53174200	Weak transcription	Fetal Heart	heart
8	chr3:53165600-53174200	Weak transcription	Left Ventricle	heart
9	chr3:53165600-53174600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:53165600-53177800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:53165600-53181400	Weak transcription	Spleen	Spleen
12	chr3:53165800-53175400	Weak transcription	Placenta	Placenta
13	chr3:53166200-53174600	Weak transcription	Primary B cells from cord blood	blood
14	chr3:53167200-53174400	Weak transcription	HMEC	breast
15	chr3:53169000-53173800	Weak transcription	Right Atrium	heart
16	chr3:53169200-53173000	Weak transcription	Liver	Liver
17	chr3:53169200-53173200	Weak transcription	Pancreas	Pancrea
18	chr3:53169200-53173400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:53169200-53174200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:53169200-53174400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:53169200-53174600	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:53169200-53176200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:53169200-53179000	Weak transcription	Fetal Lung	lung
24	chr3:53169200-53183800	Weak transcription	Right Ventricle	heart
25	chr3:53169400-53174400	Weak transcription	Hela-S3	cervix
26	chr3:53170000-53174200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:53170000-53174400	Weak transcription	Stomach Mucosa	stomach
28	chr3:53170000-53174600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:53170200-53174200	Weak transcription	Adipose Nuclei	Adipose
30	chr3:53170600-53172800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr3:53170600-53174600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:53170800-53174400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:53170800-53174400	Weak transcription	Esophagus	oesophagus
34	chr3:53171200-53172200	Enhancers	GM12878-XiMat	blood
35	chr3:53171400-53172000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr3:53171600-53172000	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr3:53171600-53173200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:53171600-53174400	Weak transcription	Lung	lung
39	chr3:53171800-53173600	Weak transcription	HepG2	liver
40	chr3:53171800-53174400	Weak transcription	Fetal Thymus	thymus

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