Variant report

Variant	rs9820125
Chromosome Location	chr3:53162279-53162280
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53160337..53170540-chr3:53189028..53198029,25	MCF-7	breast:
2	chr3:53154184..53156389-chr3:53161420..53163880,3	K562	blood:
3	chr3:53159803..53162439-chr3:53162979..53165475,2	K562	blood:
4	chr3:53156309..53158944-chr3:53161442..53163138,2	K562	blood:
5	chr3:53159864..53162439-chr3:53163975..53165914,2	K562	blood:
6	chr3:53160152..53162531-chr3:53170013..53171718,2	K562	blood:

Variant related genes	Relation type
ENSG00000163933	Chromatin interaction
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1004807	0.81[EUR][1000 genomes]
rs11130341	0.85[EUR][1000 genomes]
rs12630819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12638996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13319872	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13433700	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1560332	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2564929	0.91[ASN][1000 genomes]
rs2564944	0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28501212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28734933	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796351	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4282053	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687570	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55950520	0.91[ASN][1000 genomes]
rs56058643	0.91[ASN][1000 genomes]
rs56386026	0.91[ASN][1000 genomes]
rs57261253	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57514626	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61296683	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255925	0.91[ASN][1000 genomes]
rs62255926	0.83[ASN][1000 genomes]
rs62255929	0.91[ASN][1000 genomes]
rs62255931	0.91[ASN][1000 genomes]
rs6445565	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445566	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6769931	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6769944	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6777975	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6783748	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6784207	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792345	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792363	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799837	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6809973	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73088322	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73088327	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73088342	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7615099	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs891369	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9757079	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817467	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9820324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824325	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9828221	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9830353	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834111	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9838517	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9844531	0.86[EUR][1000 genomes]
rs9845021	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9845352	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9845484	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9858469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861744	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9867023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9867590	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9868263	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868406	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872260	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878875	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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	nsv590356	chr3:53134098-53170500	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9820125	RFT1	cis	Esophagus Muscularis	GTEx
rs9820125	RFT1	cis	Artery Tibial	GTEx
rs9820125	SERBP1P3	cis	Thyroid	GTEx
rs9820125	RFT1	cis	Artery Aorta	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53148000-53163600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:53148400-53163400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:53149600-53162400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:53152800-53163400	Weak transcription	Fetal Brain Male	brain
5	chr3:53153000-53163600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:53155600-53163400	Weak transcription	Psoas Muscle	Psoas
7	chr3:53157000-53163000	Weak transcription	Fetal Kidney	kidney
8	chr3:53157800-53163600	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr3:53157800-53163600	Weak transcription	Right Atrium	heart
10	chr3:53158200-53163000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:53158200-53163200	Weak transcription	HUVEC	blood vessel
12	chr3:53158400-53163200	Weak transcription	Stomach Mucosa	stomach
13	chr3:53158400-53163600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:53158600-53162800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:53158600-53163400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:53158600-53163400	Weak transcription	Small Intestine	intestine
17	chr3:53158600-53163600	Weak transcription	Esophagus	oesophagus
18	chr3:53158800-53163400	Weak transcription	Right Ventricle	heart
19	chr3:53159000-53163400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:53159600-53162800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:53159800-53162400	Weak transcription	Fetal Heart	heart
22	chr3:53159800-53163000	Weak transcription	Hela-S3	cervix
23	chr3:53159800-53163200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:53159800-53163200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:53159800-53163200	Weak transcription	NHDF-Ad	bronchial
26	chr3:53159800-53163400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:53159800-53163400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:53159800-53163400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:53159800-53163400	Weak transcription	Colonic Mucosa	Colon
30	chr3:53159800-53163800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:53160000-53162400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:53160000-53162400	Weak transcription	Pancreas	Pancrea
33	chr3:53160000-53162800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:53160000-53162800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:53160000-53162800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:53160000-53162800	Weak transcription	Spleen	Spleen
37	chr3:53160000-53163000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:53160000-53163000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:53160000-53163000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:53160000-53163200	Weak transcription	Brain Substantia Nigra	brain
41	chr3:53160000-53163200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:53160000-53163400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr3:53160000-53163400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:53160000-53163400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:53160000-53163400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:53160000-53163400	Weak transcription	Brain Anterior Caudate	brain
47	chr3:53160000-53163400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:53160000-53163400	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:53160000-53163400	Weak transcription	Fetal Stomach	stomach
50	chr3:53160000-53163400	Weak transcription	Gastric	stomach

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