Variant report

Variant	rs562138
Chromosome Location	chr6:49232536-49232537
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs16878901	0.80[AFR][1000 genomes]
rs16878906	0.80[AFR][1000 genomes]
rs1738322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1748805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs471258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs472168	1.00[AMR][1000 genomes]
rs473800	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs475833	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs476657	1.00[AMR][1000 genomes]
rs477529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs478469	1.00[AMR][1000 genomes]
rs480061	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs482046	1.00[AMR][1000 genomes]
rs483257	0.80[AFR][1000 genomes]
rs484612	1.00[AMR][1000 genomes]
rs485743	0.80[AFR][1000 genomes]
rs486435	1.00[AMR][1000 genomes]
rs487363	1.00[AMR][1000 genomes]
rs488497	1.00[AMR][1000 genomes]
rs489459	1.00[AMR][1000 genomes]
rs491715	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs491967	0.80[AFR][1000 genomes]
rs493691	1.00[AMR][1000 genomes]
rs494529	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs495233	1.00[AMR][1000 genomes]
rs497233	1.00[AMR][1000 genomes]
rs497390	1.00[AMR][1000 genomes]
rs498048	1.00[AMR][1000 genomes]
rs498218	1.00[AMR][1000 genomes]
rs498264	1.00[AMR][1000 genomes]
rs498367	1.00[AMR][1000 genomes]
rs498400	1.00[AMR][1000 genomes]
rs501968	1.00[AMR][1000 genomes]
rs502767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs502868	1.00[AMR][1000 genomes]
rs504940	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs505273	1.00[AMR][1000 genomes]
rs506176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs506228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs507989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs515439	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs515566	1.00[AMR][1000 genomes]
rs516988	1.00[AMR][1000 genomes]
rs517774	1.00[AMR][1000 genomes]
rs519217	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs519426	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs519734	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs520508	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs522061	1.00[AMR][1000 genomes]
rs523440	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs523897	1.00[AMR][1000 genomes]
rs524781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs524822	1.00[AMR][1000 genomes]
rs525102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs525892	1.00[AMR][1000 genomes]
rs529393	1.00[AMR][1000 genomes]
rs530710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs531943	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs539366	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs540175	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs540374	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs541985	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs544714	0.81[YRI][hapmap]
rs546248	1.00[AMR][1000 genomes]
rs547267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs547609	1.00[AMR][1000 genomes]
rs550330	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs550485	1.00[AMR][1000 genomes]
rs550645	1.00[AMR][1000 genomes]
rs552336	1.00[AMR][1000 genomes]
rs552350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs552383	1.00[AMR][1000 genomes]
rs553567	1.00[AMR][1000 genomes]
rs554083	1.00[AMR][1000 genomes]
rs556318	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs558669	1.00[AMR][1000 genomes]
rs559388	1.00[AMR][1000 genomes]
rs559706	1.00[AMR][1000 genomes]
rs560390	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs560700	1.00[AMR][1000 genomes]
rs561215	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs561296	1.00[AMR][1000 genomes]
rs562011	1.00[AMR][1000 genomes]
rs563878	1.00[AMR][1000 genomes]
rs564151	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs565702	1.00[AMR][1000 genomes]
rs565793	1.00[AMR][1000 genomes]
rs567539	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs571802	0.80[AFR][1000 genomes]
rs572782	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs574868	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs574970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs575753	1.00[AMR][1000 genomes]
rs577075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs577922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs578848	1.00[AMR][1000 genomes]
rs579011	1.00[AMR][1000 genomes]
rs6933384	0.94[AFR][1000 genomes];1.00[AMR][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	nsv949690	chr6:48595821-49289855	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2755862	chr6:49081541-49298041	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 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	chr6:49232200-49232800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:49232200-49232800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:49232200-49232800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:49232200-49233000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:49232200-49233000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:49232200-49233000	Bivalent/Poised TSS	HepG2	liver
7	chr6:49232200-49233000	Enhancers	HMEC	breast
8	chr6:49232400-49233200	ZNF genes & repeats	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links