Variant report

Variant	rs17878691
Chromosome Location	chr1:153004684-153004685
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	ATF2	chr1:153004515-153004838	GM12878	blood:	n/a	n/a
2	RUNX3	chr1:153004442-153004973	GM12878	blood:	n/a	n/a
3	RUNX3	chr1:153004443-153004901	GM12878	blood:	n/a	n/a
4	PAX5	chr1:153004551-153005023	GM12878	blood:	n/a	n/a
5	PAX5	chr1:153004511-153004909	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SPRR1B	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10494283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10494284	1.00[AMR][1000 genomes]
rs10494286	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10494287	1.00[AMR][1000 genomes]
rs10494289	1.00[AMR][1000 genomes]
rs1611758	1.00[AMR][1000 genomes]
rs1611769	1.00[AMR][1000 genomes]
rs16829001	1.00[AMR][1000 genomes]
rs16829018	0.89[ASW][hapmap];0.86[LWK][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16834786	1.00[AMR][1000 genomes]
rs16834788	1.00[AMR][1000 genomes]
rs16834793	1.00[AMR][1000 genomes]
rs16834804	1.00[AMR][1000 genomes]
rs16834825	1.00[AMR][1000 genomes]
rs16834841	1.00[AMR][1000 genomes]
rs16834843	1.00[AMR][1000 genomes]
rs16834855	1.00[AMR][1000 genomes]
rs16834863	0.81[ASW][hapmap];0.86[LWK][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16834869	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16834878	0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16834888	0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16834890	1.00[ASW][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17882151	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17883580	1.00[AMR][1000 genomes]
rs1933385	1.00[AMR][1000 genomes]
rs1933387	1.00[AMR][1000 genomes]
rs1998818	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28924715	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3806220	1.00[AMR][1000 genomes]
rs3899406	1.00[ASW][hapmap];0.85[YRI][hapmap]
rs3964618	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4378151	1.00[AMR][1000 genomes]
rs4433340	0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57055311	1.00[AMR][1000 genomes]
rs57242863	1.00[AMR][1000 genomes]
rs57450008	1.00[AMR][1000 genomes]
rs57458543	1.00[AMR][1000 genomes]
rs58109785	1.00[AMR][1000 genomes]
rs58783614	1.00[AMR][1000 genomes]
rs59237147	1.00[AMR][1000 genomes]
rs59460179	1.00[AMR][1000 genomes]
rs61089580	1.00[AMR][1000 genomes]
rs73010427	1.00[AMR][1000 genomes]
rs73010429	1.00[AMR][1000 genomes]
rs73010443	1.00[AMR][1000 genomes]
rs73010447	1.00[AMR][1000 genomes]
rs73010449	1.00[AMR][1000 genomes]
rs73010452	1.00[AMR][1000 genomes]
rs73010454	1.00[AMR][1000 genomes]
rs73010458	1.00[AMR][1000 genomes]
rs73010459	1.00[AMR][1000 genomes]
rs73012481	1.00[AMR][1000 genomes]
rs73012485	1.00[AMR][1000 genomes]
rs73012496	1.00[AMR][1000 genomes]
rs73012500	1.00[AMR][1000 genomes]
rs73014324	1.00[AMR][1000 genomes]
rs73014333	1.00[AMR][1000 genomes]
rs73014337	1.00[AMR][1000 genomes]
rs73014398	1.00[AMR][1000 genomes]
rs73014402	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73016303	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73016322	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs883809	1.00[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	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv1003756	chr1:152944201-153044621	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	esv3416199	chr1:152957887-153005113	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153003200-153008200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:153003400-153006200	Flanking Active TSS	NHEK	skin
3	chr1:153003600-153005400	Flanking Active TSS	HMEC	breast
4	chr1:153003600-153005600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:153003800-153004800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:153003800-153005400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links