Variant report

Variant	rs709389
Chromosome Location	chr5:98329715-98329716
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98286475..98288503-chr5:98329447..98332320,2	MCF-7	breast:

Extended variants
information (count: 147 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10037147	0.82[ASN][1000 genomes]
rs10038192	0.95[ASN][1000 genomes]
rs10040066	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10041261	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10050423	0.97[ASN][1000 genomes]
rs10050804	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10076291	0.87[ASN][1000 genomes]
rs10477857	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10479345	0.87[ASN][1000 genomes]
rs10479346	0.87[ASN][1000 genomes]
rs10479348	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1093794	0.95[ASN][1000 genomes]
rs1104262	0.95[ASN][1000 genomes]
rs11242567	1.00[CHB][hapmap]
rs11242574	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11242579	0.90[JPT][hapmap]
rs11745405	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11949103	0.87[ASN][1000 genomes]
rs11950452	0.87[ASN][1000 genomes]
rs11950855	0.82[ASN][1000 genomes]
rs11960896	0.87[ASN][1000 genomes]
rs12189335	0.87[ASN][1000 genomes]
rs12515042	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13179812	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1472622	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs151102	1.00[CHB][hapmap]
rs1604450	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs161729	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161730	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161731	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs161732	1.00[CHB][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs161935	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs161936	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs162341	0.93[ASN][1000 genomes]
rs167798	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17166527	0.82[AFR][1000 genomes]
rs17166529	0.82[AFR][1000 genomes]
rs17166530	0.82[AFR][1000 genomes]
rs17166548	0.82[AFR][1000 genomes]
rs17166551	0.82[AFR][1000 genomes]
rs172874	0.93[ASN][1000 genomes]
rs1875529	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2221268	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2455423	0.95[ASN][1000 genomes]
rs246251	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2927647	0.93[ASN][1000 genomes]
rs2927648	0.95[ASN][1000 genomes]
rs2927654	0.95[ASN][1000 genomes]
rs2937706	0.95[ASN][1000 genomes]
rs2937708	0.95[ASN][1000 genomes]
rs2937709	0.95[ASN][1000 genomes]
rs325195	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs325220	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs326480	1.00[CHB][hapmap]
rs326481	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs326482	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs326493	0.93[ASN][1000 genomes]
rs327807	1.00[CHB][hapmap]
rs34488	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34489	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs34490	0.95[ASN][1000 genomes]
rs34491	0.93[ASN][1000 genomes]
rs34496	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs34497	0.93[ASN][1000 genomes]
rs34498	1.00[CHB][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs363929	0.97[ASN][1000 genomes]
rs366000	0.95[ASN][1000 genomes]
rs366353	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs370529	0.93[ASN][1000 genomes]
rs377731	0.90[JPT][hapmap]
rs378089	0.95[ASN][1000 genomes]
rs380156	0.95[ASN][1000 genomes]
rs393697	0.95[ASN][1000 genomes]
rs395668	0.93[ASN][1000 genomes]
rs39660	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs398436	0.95[ASN][1000 genomes]
rs40075	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs407562	0.95[ASN][1000 genomes]
rs416750	1.00[ASN][1000 genomes]
rs422127	0.95[ASN][1000 genomes]
rs434039	0.95[ASN][1000 genomes]
rs4343864	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs443726	0.95[ASN][1000 genomes]
rs447044	1.00[ASN][1000 genomes]
rs449204	0.95[ASN][1000 genomes]
rs451141	0.95[ASN][1000 genomes]
rs4565239	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs4583911	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs45931	0.95[ASN][1000 genomes]
rs467728	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs4703049	1.00[ASN][1000 genomes]
rs4703052	0.87[ASN][1000 genomes]
rs4703340	0.87[ASN][1000 genomes]
rs4703345	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs539024	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55918054	0.82[AFR][1000 genomes]
rs559574	0.95[ASN][1000 genomes]
rs56393810	0.82[AFR][1000 genomes]
rs59602127	0.81[AFR][1000 genomes]
rs60347076	0.82[AFR][1000 genomes]
rs60955929	0.82[AFR][1000 genomes]
rs6878136	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs709386	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709387	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709388	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709390	1.00[ASN][1000 genomes]
rs73155495	0.82[AFR][1000 genomes]
rs73155497	0.82[AFR][1000 genomes]
rs73155499	0.82[AFR][1000 genomes]
rs73157406	0.82[AFR][1000 genomes]
rs73157408	0.82[AFR][1000 genomes]
rs73157409	0.82[AFR][1000 genomes]
rs73157411	0.82[AFR][1000 genomes]
rs73157413	0.80[AFR][1000 genomes]
rs73157414	0.82[AFR][1000 genomes]
rs73157416	0.82[AFR][1000 genomes]
rs73157417	0.80[AFR][1000 genomes]
rs73157423	0.82[AFR][1000 genomes]
rs73157487	0.82[AFR][1000 genomes]
rs73157490	0.82[AFR][1000 genomes]
rs7449447	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7701147	0.83[AFR][1000 genomes]
rs7705736	0.82[AFR][1000 genomes]
rs7710032	1.00[ASN][1000 genomes]
rs7711061	1.00[ASN][1000 genomes]
rs7711225	0.82[AFR][1000 genomes]
rs7712408	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7717324	0.90[JPT][hapmap]
rs7717482	0.92[LWK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs7717655	0.83[AFR][1000 genomes]
rs7719562	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7719649	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7723242	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7726071	0.82[AFR][1000 genomes]
rs7727357	0.82[AFR][1000 genomes]
rs7727987	0.82[AFR][1000 genomes]
rs7728879	0.82[AFR][1000 genomes]
rs819227	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs819230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs819231	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs819232	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826071	chr5:98312447-98358852	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv1827754	chr5:98312447-98358852	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv1837772	chr5:98312447-98358852	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv1838335	chr5:98312447-98358852	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1845131	chr5:98312447-98358852	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv4930	chr5:98318768-98350644	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs709389	SLCO4C1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98326200-98331600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:98328000-98330600	Enhancers	Thymus	Thymus
3	chr5:98328600-98330800	Enhancers	Fetal Thymus	thymus
4	chr5:98329000-98331800	Enhancers	Stomach Mucosa	stomach
5	chr5:98329200-98329800	Enhancers	K562	blood
6	chr5:98329200-98330600	Enhancers	Gastric	stomach
7	chr5:98329400-98329800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:98329400-98329800	Enhancers	Placenta	Placenta
9	chr5:98329400-98330000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:98329400-98330800	Enhancers	Fetal Intestine Large	intestine
11	chr5:98329600-98329800	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links