Variant report

Variant	rs294482
Chromosome Location	chr5:58845915-58845916
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58843792..58846510-chr5:58858792..58861752,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10805516	0.84[ASN][1000 genomes]
rs159194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159196	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159197	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs177077	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs186078	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs190936	0.84[ASN][1000 genomes]
rs294477	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs294478	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs294479	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs294481	0.92[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs294483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs294484	1.00[CHB][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs294485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs294486	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs294492	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs294494	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294495	0.89[ASN][1000 genomes]
rs294496	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs294497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs294498	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs294499	0.93[ASN][1000 genomes]
rs294500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs294501	0.92[ASN][1000 genomes]
rs294502	0.93[ASN][1000 genomes]
rs295943	0.85[ASW][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs295946	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs295948	0.88[ASN][1000 genomes]
rs295950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295951	0.88[ASN][1000 genomes]
rs295952	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs295953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295954	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295955	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs295956	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295957	0.88[ASN][1000 genomes]
rs295958	0.87[ASN][1000 genomes]
rs295960	0.87[ASN][1000 genomes]
rs295962	0.84[ASN][1000 genomes]
rs295963	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs295964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs295965	0.84[ASN][1000 genomes]
rs295966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs295967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs295968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs295969	0.84[ASN][1000 genomes]
rs295970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs295971	0.84[ASN][1000 genomes]
rs295972	0.84[ASN][1000 genomes]
rs295973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs295974	0.84[ASN][1000 genomes]
rs295975	0.84[ASN][1000 genomes]
rs295978	0.91[ASN][1000 genomes]
rs295979	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs295980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs298014	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs298016	0.84[ASN][1000 genomes]
rs298017	0.84[ASN][1000 genomes]
rs298025	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298027	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298028	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298029	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298030	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298032	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs298033	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298034	0.92[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs298038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs298039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs298040	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs298043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs298044	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs298045	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs298046	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs298048	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298051	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs298052	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs298053	0.84[ASN][1000 genomes]
rs37569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs37570	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs37571	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv462189	chr5:58830145-58879822	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv598255	chr5:58830145-58879822	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs294482	FLJ37543	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58836600-58854400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:58836800-58857400	Weak transcription	Primary B cells from cord blood	blood
3	chr5:58840000-58851600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:58840200-58849000	Weak transcription	Fetal Intestine Small	intestine
5	chr5:58840200-58849800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:58840200-58858800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:58840400-58850800	Weak transcription	Brain Substantia Nigra	brain
8	chr5:58840400-58853200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr5:58840400-58856200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:58840600-58851400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:58840800-58858600	Weak transcription	Fetal Kidney	kidney
12	chr5:58843800-58862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:58844000-58851600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr5:58844400-58854600	Weak transcription	Fetal Lung	lung
15	chr5:58844800-58851400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:58844800-58854400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:58845000-58849000	Weak transcription	Psoas Muscle	Psoas
18	chr5:58845200-58847000	Flanking Active TSS	A549	lung
19	chr5:58845200-58849800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr5:58845200-58850200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:58845200-58856200	Weak transcription	Hela-S3	cervix
22	chr5:58845600-58858200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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