Variant report

Variant	rs62255890
Chromosome Location	chr3:53046496-53046497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53045411..53048406-chr3:53050370..53052257,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11130333	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130335	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12053904	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12633064	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12635933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17304694	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1811351	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2115779	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2336720	0.95[ASN][1000 genomes]
rs2336721	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2564929	0.83[AMR][1000 genomes]
rs2564939	0.84[AMR][1000 genomes]
rs2581798	0.82[AMR][1000 genomes]
rs35671032	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55796351	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55950520	0.86[AMR][1000 genomes]
rs55962821	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56026870	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs56058643	0.84[AMR][1000 genomes]
rs56129941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56155510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56384586	0.97[ASN][1000 genomes]
rs56386026	0.83[AMR][1000 genomes]
rs57916015	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62253602	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62253603	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62253604	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62253606	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62253608	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62253649	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62253656	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62255895	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62255897	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62255898	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62255925	0.84[AMR][1000 genomes]
rs62255929	0.84[AMR][1000 genomes]
rs62255931	0.84[AMR][1000 genomes]
rs6781896	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73079924	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73082047	0.84[AMR][1000 genomes]
rs73087044	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9823865	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv3823	chr3:53003659-53051063	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv876799	chr3:53024216-53060637	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv437713	chr3:53026714-53055522	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv590320	chr3:53027983-53055842	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv590321	chr3:53027983-53062661	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1000733	chr3:53031724-53053645	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv2489889	chr3:53045787-53048331	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs62255890	RFT1	cis	Thyroid	GTEx
rs62255890	RFT1	cis	Artery Aorta	GTEx
rs62255890	SERBP1P3	cis	Esophagus Muscularis	GTEx
rs62255890	SERBP1P3	cis	Skin Sun Exposed Lower leg	GTEx
rs62255890	SERBP1P3	cis	lung	GTEx
rs62255890	SERBP1P3	cis	Thyroid	GTEx
rs62255890	RFT1	cis	Esophagus Muscularis	GTEx
rs62255890	RFT1	cis	Artery Tibial	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53019000-53057200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:53019600-53056400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:53020600-53057000	Weak transcription	Dnd41	blood
4	chr3:53022600-53050400	Weak transcription	Primary B cells from cord blood	blood
5	chr3:53025600-53061600	Weak transcription	Lung	lung
6	chr3:53027600-53061600	Weak transcription	Liver	Liver
7	chr3:53027800-53051000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:53030200-53059400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:53030400-53052400	Weak transcription	Primary T cells from cord blood	blood
10	chr3:53030800-53050400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:53032800-53051600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:53033000-53078400	Weak transcription	Aorta	Aorta
13	chr3:53033200-53057000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:53033600-53056200	Weak transcription	Fetal Stomach	stomach
15	chr3:53033800-53052800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:53033800-53053800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:53033800-53060400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:53033800-53065000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:53037000-53065000	Weak transcription	Fetal Intestine Small	intestine
20	chr3:53040800-53065000	Weak transcription	Fetal Intestine Large	intestine
21	chr3:53041400-53053600	Weak transcription	Fetal Thymus	thymus
22	chr3:53043800-53064800	Weak transcription	Stomach Mucosa	stomach
23	chr3:53044400-53050400	Weak transcription	A549	lung
24	chr3:53044400-53052400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:53044400-53056000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:53044600-53048800	Weak transcription	Pancreas	Pancrea
27	chr3:53044600-53050200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:53044600-53051200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:53044600-53055600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:53044600-53065000	Weak transcription	Gastric	stomach
31	chr3:53045000-53050400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr3:53045200-53049800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:53045200-53050200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:53045200-53050200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:53045200-53061400	Weak transcription	Fetal Heart	heart
36	chr3:53045400-53049600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:53045400-53050200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr3:53045400-53052600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:53045400-53057200	Weak transcription	Psoas Muscle	Psoas
40	chr3:53045400-53061600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:53045600-53050600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:53045600-53052400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr3:53045600-53057000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:53045600-53057600	Weak transcription	Left Ventricle	heart
45	chr3:53045800-53050400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:53045800-53061400	Weak transcription	HepG2	liver
47	chr3:53046000-53051800	Weak transcription	GM12878-XiMat	blood
48	chr3:53046000-53052400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:53046000-53057600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:53046200-53052600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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