Variant report

Variant	rs6884507
Chromosome Location	chr5:40672844-40672845
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40667749..40669550-chr5:40672686..40674333,2	MCF-7	breast:
2	chr5:40671388..40674176-chr5:40680910..40682614,2	MCF-7	breast:
3	chr5:40671624..40675348-chr5:40676971..40680818,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171522	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10035697	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10038251	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10038367	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10039983	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10043839	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10043891	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10044538	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10053469	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10056173	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10057182	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10065482	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10065874	0.82[ASN][1000 genomes]
rs10066459	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068069	0.84[ASN][1000 genomes]
rs10071870	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10074117	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10473206	0.82[ASN][1000 genomes]
rs10473209	0.81[ASN][1000 genomes]
rs10473210	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10473211	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10473212	0.81[AMR][1000 genomes]
rs10473214	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10473216	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10941521	0.82[ASN][1000 genomes]
rs10941522	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11744569	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11949581	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12188666	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12513529	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1553578	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1553579	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17835256	0.85[ASN][1000 genomes]
rs35693860	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs45437592	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4599576	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4957334	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4957336	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4957337	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4957338	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4957339	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4957343	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62356460	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62356461	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62358056	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62358796	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62358800	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6860233	0.82[ASN][1000 genomes]
rs72747928	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72747930	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72747940	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9292784	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9292785	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6884507	RPL37	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40667600-40676000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr5:40668200-40675800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr5:40668600-40677600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr5:40668800-40673800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr5:40668800-40677200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr5:40668800-40678600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:40669000-40674000	Enhancers	Primary hematopoietic stem cells	blood
8	chr5:40669800-40676800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:40670000-40674400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr5:40670600-40674600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr5:40670800-40673400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr5:40670800-40674000	Weak transcription	Stomach Mucosa	stomach
13	chr5:40670800-40675800	Enhancers	Primary T cells from cord blood	blood
14	chr5:40671000-40674800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr5:40671400-40674800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:40671400-40676000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:40671600-40673200	Enhancers	Primary B cells from cord blood	blood
18	chr5:40672000-40673800	Enhancers	Fetal Thymus	thymus
19	chr5:40672000-40678400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr5:40672200-40673000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr5:40672400-40673000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:40672400-40673200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr5:40672400-40673400	Enhancers	Primary B cells from peripheral blood	blood
24	chr5:40672400-40674000	Enhancers	Thymus	Thymus
25	chr5:40672400-40677000	Weak transcription	HSMMtube	muscle
26	chr5:40672600-40673400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:40672600-40673400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:40672600-40673400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:40672600-40675600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr5:40672600-40676200	Enhancers	Dnd41	blood
31	chr5:40672600-40676800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:40672600-40678600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:40672800-40673600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr5:40672800-40673600	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr5:40672800-40673600	Enhancers	Hela-S3	cervix
36	chr5:40672800-40678600	Enhancers	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links