Variant report

Variant	rs60676487
Chromosome Location	chr19:40171810-40171811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:40168990-40172822	GM12878	blood:	n/a	n/a
2	STAT5A	chr19:40169635-40172036	GM12878	blood:	n/a	chr19:40169874-40169885 chr19:40170203-40170214
3	POLR2A	chr19:40171784-40172356	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:40169120-40172570	GM12878	blood:	n/a	n/a
5	EBF1	chr19:40168815-40171812	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:40171747-40172183	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:40169083-40172673	GM12878	blood:	n/a	n/a
8	MTA3	chr19:40168531-40172519	GM12878	blood:	n/a	n/a
9	STAT5A	chr19:40169134-40172621	GM12878	blood:	n/a	chr19:40172551-40172563 chr19:40169874-40169885 chr19:40172037-40172049 chr19:40170203-40170214
10	POLR2A	chr19:40169672-40171847	GM12878	blood:	n/a	n/a
11	NFATC1	chr19:40169041-40171846	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:40169221-40172689	GM18505	blood:	n/a	n/a
13	NFATC1	chr19:40171347-40171918	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40168776..40170659-chr19:40171070..40173926,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269460	TF binding region
ENSG00000226025	TF binding region
ENSG00000226025	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10402453	1.00[ASN][1000 genomes]
rs10415800	1.00[ASN][1000 genomes]
rs10416515	1.00[ASN][1000 genomes]
rs16973571	1.00[ASN][1000 genomes]
rs16973572	1.00[ASN][1000 genomes]
rs56960663	1.00[ASN][1000 genomes]
rs57205516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57758462	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58988184	1.00[ASN][1000 genomes]
rs59155776	1.00[ASN][1000 genomes]
rs59747400	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60628785	1.00[ASN][1000 genomes]
rs61346225	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61737337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73557810	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73557829	1.00[ASN][1000 genomes]
rs73557849	1.00[ASN][1000 genomes]
rs73557862	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73557894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73559714	1.00[AMR][1000 genomes]
rs73559726	1.00[AMR][1000 genomes]
rs8104205	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107384	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057361	chr19:40123868-40310996	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv3413868	chr19:40130700-40184720	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1061361	chr19:40131820-40310996	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv579511	chr19:40132825-40310497	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1062394	chr19:40133229-40310186	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv544004	chr19:40133229-40310186	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv3355956	chr19:40135051-40188792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv3998	chr19:40135120-40188646	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	esv3397881	chr19:40150495-40199437	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv1059691	chr19:40168862-40306373	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv544005	chr19:40168862-40306373	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv960763	chr19:40168890-40177573	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40168600-40172600	Flanking Active TSS	GM12878-XiMat	blood
2	chr19:40170000-40184600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:40171200-40172400	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr19:40171200-40189000	Weak transcription	Psoas Muscle	Psoas
5	chr19:40171400-40172000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr19:40171600-40172000	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr19:40171800-40172000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr19:40171800-40177600	Weak transcription	Fetal Muscle Leg	muscle

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