Variant report

Variant	rs42245
Chromosome Location	chr5:93698668-93698669
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	chr5:93693342..93695465-chr5:93695922..93698858,2	MCF-7	breast:
2	chr5:93690372..93692897-chr5:93696363..93699335,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10463187	0.81[AMR][1000 genomes]
rs10491400	0.81[AMR][1000 genomes]
rs11749838	0.81[AMR][1000 genomes]
rs12660022	0.84[AMR][1000 genomes]
rs160268	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs160270	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs160272	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs160273	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs160275	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17082131	0.81[AMR][1000 genomes]
rs17083516	0.81[AMR][1000 genomes]
rs17083564	0.81[AMR][1000 genomes]
rs17083566	0.81[AMR][1000 genomes]
rs1841300	0.84[AMR][1000 genomes]
rs1841301	0.83[AMR][1000 genomes]
rs2434364	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2446772	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2914322	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2926571	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs29951	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs29952	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29953	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs29959	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs29960	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs29961	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs29962	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs366404	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs39810	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs401521	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs405029	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs412437	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs424374	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs429519	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs431283	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs442817	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs443577	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs447540	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs485494	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6859083	0.81[AMR][1000 genomes]
rs7705823	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7706373	0.83[AMR][1000 genomes]
rs9763486	0.84[AMR][1000 genomes]
rs9764893	0.84[AMR][1000 genomes]
rs979264	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023191	chr5:93351646-93947928	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv537808	chr5:93351646-93947928	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases
3	esv2753025	chr5:93356544-93812844	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1027890	chr5:93584978-93873704	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv537809	chr5:93584978-93873704	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv518161	chr5:93643170-93789309	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv523867	chr5:93643170-93789309	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv598950	chr5:93666346-93788579	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv1023421	chr5:93679661-93911066	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93674200-93716400	Weak transcription	Hela-S3	cervix
2	chr5:93682200-93775800	Weak transcription	Ovary	ovary
3	chr5:93696400-93765400	Weak transcription	Aorta	Aorta
4	chr5:93697600-93698800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:93697600-93698800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:93697600-93698800	Enhancers	HMEC	breast
7	chr5:93697600-93699400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:93697800-93698800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr5:93698000-93707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:93698200-93698800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr5:93698200-93699200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr5:93698200-93699200	Enhancers	Stomach Mucosa	stomach
13	chr5:93698400-93698800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr5:93698400-93698800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr5:93698400-93702000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:93698600-93698800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr5:93698600-93698800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr5:93698600-93699200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr5:93698600-93699200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr5:93698600-93699600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:93698600-93699800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:93698600-93702200	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links