Variant report

Variant	rs16877888
Chromosome Location	chr5:59604903-59604904
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	chr5:59604743-59605203	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
RNU6-806P	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs16877866	1.00[YRI][hapmap]
rs16877868	1.00[YRI][hapmap]
rs16877877	0.88[YRI][hapmap]
rs16877886	1.00[YRI][hapmap]
rs16877887	1.00[YRI][hapmap]
rs16877890	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16877893	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16877895	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs34114616	0.86[AFR][1000 genomes]
rs35250060	0.88[AFR][1000 genomes]
rs4460096	0.80[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57172565	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs60693366	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61497235	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6869344	1.00[YRI][hapmap]
rs6874690	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6875020	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6891047	0.87[AMR][1000 genomes]
rs6892680	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73104776	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73104780	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73104781	0.87[AMR][1000 genomes]
rs73106708	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73106740	0.87[AMR][1000 genomes]
rs73106742	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73106751	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73106753	0.87[AMR][1000 genomes]
rs73106756	0.96[AFR][1000 genomes]
rs73106759	0.87[AMR][1000 genomes]
rs73106769	0.87[AMR][1000 genomes]
rs73106773	0.87[AMR][1000 genomes]
rs73106774	0.87[AMR][1000 genomes]
rs73106777	0.87[AMR][1000 genomes]
rs7711198	0.87[YRI][hapmap]
rs7712352	0.94[AFR][1000 genomes]
rs7712697	0.90[AFR][1000 genomes]
rs7718384	1.00[YRI][hapmap];0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv830316	chr5:59480269-59689829	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59604400-59605000	Enhancers	HepG2	liver
2	chr5:59604400-59605600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr5:59604400-59605600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr5:59604400-59605600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr5:59604600-59605200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr5:59604600-59605200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:59604600-59605200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:59604600-59605200	Enhancers	Fetal Brain Male	brain
9	chr5:59604800-59605200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr5:59604800-59605400	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr5:59604800-59605600	Enhancers	HUES48 Cell Line	embryonic stem cell

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