Variant report

Variant	rs1553578
Chromosome Location	chr5:40669184-40669185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:40667749..40669550-chr5:40672686..40674333,2	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10035235	0.94[JPT][hapmap]
rs10035697	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10038251	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10038367	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10039983	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10040364	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10043839	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10043891	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10044538	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10053469	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10053664	0.94[JPT][hapmap]
rs10055624	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10056173	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10057182	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10062565	0.84[JPT][hapmap]
rs10063818	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10063864	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10065482	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10065874	0.83[ASN][1000 genomes]
rs10065894	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10066459	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10068069	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10069737	0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap]
rs10071870	0.96[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10073344	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10074117	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1015027	0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap]
rs10473206	0.83[ASN][1000 genomes]
rs10473209	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10473210	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10473211	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10473212	0.84[AMR][1000 genomes]
rs10473214	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10473216	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10941521	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10941522	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10941525	0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap]
rs11744569	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11744700	0.82[ASN][1000 genomes]
rs11745462	0.80[AFR][1000 genomes]
rs11747210	0.89[GIH][hapmap];0.94[JPT][hapmap]
rs11949581	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11952914	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11955037	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11957406	0.80[CEU][hapmap]
rs12188666	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12513529	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12517210	0.91[GIH][hapmap];0.94[JPT][hapmap]
rs12520058	1.00[JPT][hapmap];0.92[YRI][hapmap]
rs12523329	1.00[JPT][hapmap]
rs1363847	1.00[JPT][hapmap];0.91[YRI][hapmap]
rs1395082	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1553579	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17238368	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17835256	0.85[ASN][1000 genomes]
rs2270625	0.84[JPT][hapmap]
rs2291782	0.84[JPT][hapmap]
rs35693860	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3792827	1.00[JPT][hapmap];0.92[YRI][hapmap]
rs3805489	0.94[JPT][hapmap]
rs3805490	0.94[JPT][hapmap]
rs3805492	0.94[JPT][hapmap]
rs3805494	0.94[JPT][hapmap]
rs3805499	1.00[JPT][hapmap]
rs3816959	0.84[JPT][hapmap]
rs45437592	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4599576	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4957334	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4957336	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4957337	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4957338	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4957339	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4957343	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4957347	0.81[AFR][1000 genomes]
rs62356460	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62356461	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62358056	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62358796	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62358800	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6860233	0.83[ASN][1000 genomes]
rs6867169	0.82[ASN][1000 genomes]
rs6868112	0.84[GIH][hapmap];0.84[JPT][hapmap]
rs6879155	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6879329	0.82[ASN][1000 genomes]
rs6884507	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72747928	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72747930	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72747940	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7349788	0.82[ASN][1000 genomes]
rs7719692	1.00[JPT][hapmap];0.92[YRI][hapmap]
rs7721093	1.00[JPT][hapmap];0.92[YRI][hapmap]
rs7725810	0.84[JPT][hapmap]
rs7726047	0.82[ASN][1000 genomes]
rs9292784	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9292785	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880993	chr5:40521648-40682550	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
2	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1553578	FBLL1	trans	cerebellum	SCAN
rs1553578	RPL37	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40655600-40669600	Weak transcription	Thymus	Thymus
2	chr5:40666000-40669200	Weak transcription	Fetal Thymus	thymus
3	chr5:40667600-40676000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr5:40667800-40671200	Weak transcription	Hela-S3	cervix
5	chr5:40668200-40675800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr5:40668600-40677600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr5:40668800-40669200	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr5:40668800-40669800	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr5:40668800-40669800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:40668800-40670400	Enhancers	Primary T cells from cord blood	blood
11	chr5:40668800-40671000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:40668800-40671400	Enhancers	Dnd41	blood
13	chr5:40668800-40673800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr5:40668800-40677200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:40668800-40678600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:40669000-40670400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr5:40669000-40670800	Enhancers	Primary B cells from cord blood	blood
18	chr5:40669000-40670800	Enhancers	Stomach Mucosa	stomach
19	chr5:40669000-40671000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr5:40669000-40671000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:40669000-40671000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr5:40669000-40674000	Enhancers	Primary hematopoietic stem cells	blood

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