Variant report

Variant	rs2052553
Chromosome Location	chr5:90729906-90729907
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	chr5:90725441..90728482-chr5:90729340..90730983,3	K562	blood:
2	chr5:90677477..90679457-chr5:90727300..90730870,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10041402	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10045280	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10052492	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10054820	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10058025	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10059163	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10063683	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10073657	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10073935	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035476	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1035477	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10474352	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10474353	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10942634	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11948056	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11948075	0.95[EUR][1000 genomes]
rs11950530	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11955120	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11959525	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12110065	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12110303	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12188467	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12651840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654787	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12655973	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12656350	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1363839	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1477348	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1477349	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs186717	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1895448	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1895449	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1964292	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1966494	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2004483	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2059207	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059208	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2367353	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2367526	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2839728	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2887007	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs332529	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs332531	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs332544	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35712350	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4382199	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60513756	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6452951	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6452953	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6452954	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66759971	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6860948	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6865495	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6866191	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6866923	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6867091	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869048	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6869717	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6882269	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs746637	0.95[EUR][1000 genomes]
rs7705465	0.95[EUR][1000 genomes]
rs7708782	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7715402	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7718871	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7720132	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7720235	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs889213	0.95[EUR][1000 genomes]
rs9293568	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9686361	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs985434	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1030453	chr5:90709080-90849693	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90726800-90737400	Weak transcription	Esophagus	oesophagus
2	chr5:90728800-90730000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
3	chr5:90729000-90730200	Enhancers	Primary T cells fromperipheralblood	blood
4	chr5:90729000-90730200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:90729000-90731800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr5:90729000-90733600	Weak transcription	Stomach Mucosa	stomach
7	chr5:90729200-90730200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr5:90729200-90731400	Enhancers	Primary T cells from cord blood	blood
9	chr5:90729200-90731400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr5:90729200-90731600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:90729200-90731600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr5:90729200-90732400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr5:90729400-90731400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr5:90729400-90731800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:90729600-90730200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:90729600-90730200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:90729600-90730600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:90729600-90731400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr5:90729600-90731600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr5:90729800-90730200	Enhancers	Fetal Thymus	thymus
21	chr5:90729800-90730400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:90729800-90730600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr5:90729800-90730600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr5:90729800-90730600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:90729800-90730600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr5:90729800-90731000	Enhancers	HUES48 Cell Line	embryonic stem cell

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