Variant report

Variant	rs12408689
Chromosome Location	chr1:210285308-210285309
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10489346	0.90[AMR][1000 genomes]
rs10779520	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10779521	0.93[AMR][1000 genomes]
rs10863796	1.00[EUR][1000 genomes]
rs10863801	1.00[EUR][1000 genomes]
rs10863806	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10863809	0.93[AMR][1000 genomes]
rs10863814	0.93[AMR][1000 genomes]
rs11119361	1.00[EUR][1000 genomes]
rs11119362	1.00[EUR][1000 genomes]
rs11119371	0.90[CHB][hapmap];0.80[AMR][1000 genomes]
rs11119372	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11119384	0.81[AMR][1000 genomes]
rs11119388	0.81[AMR][1000 genomes]
rs11119391	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11119394	0.84[AMR][1000 genomes]
rs11119398	0.90[AMR][1000 genomes]
rs11119401	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11119403	0.93[AMR][1000 genomes]
rs11119417	0.98[AMR][1000 genomes]
rs11119433	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11119434	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11119442	0.82[AMR][1000 genomes]
rs12057832	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12059828	0.93[AMR][1000 genomes]
rs12061641	0.93[AMR][1000 genomes]
rs12062530	0.84[AMR][1000 genomes]
rs12064990	1.00[EUR][1000 genomes]
rs12065575	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12066358	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12067807	1.00[EUR][1000 genomes]
rs12069592	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12073617	0.93[AMR][1000 genomes]
rs12078802	0.81[AMR][1000 genomes]
rs12079812	1.00[EUR][1000 genomes]
rs12079916	0.97[AMR][1000 genomes]
rs12084199	0.81[AMR][1000 genomes]
rs12085177	0.81[AMR][1000 genomes]
rs12088422	0.93[AMR][1000 genomes]
rs12089327	0.98[AMR][1000 genomes]
rs12089449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12092527	0.98[AMR][1000 genomes]
rs12094309	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12094626	0.81[AMR][1000 genomes]
rs12401574	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12403002	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12403098	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12405601	0.81[AMR][1000 genomes]
rs12406136	0.92[AMR][1000 genomes]
rs12407647	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12409047	0.98[AMR][1000 genomes]
rs12409069	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12409582	0.90[CHB][hapmap]
rs12565072	0.84[AMR][1000 genomes]
rs12566105	0.97[AMR][1000 genomes]
rs12566314	0.84[AMR][1000 genomes]
rs12569033	0.93[AMR][1000 genomes]
rs1387932	0.93[AMR][1000 genomes]
rs17015564	0.93[AMR][1000 genomes]
rs17015565	0.93[AMR][1000 genomes]
rs17015566	0.93[AMR][1000 genomes]
rs17015667	0.97[AMR][1000 genomes]
rs2130625	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2130629	0.98[AMR][1000 genomes]
rs2273047	1.00[EUR][1000 genomes]
rs28417505	0.98[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4844507	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844509	0.97[AMR][1000 genomes]
rs4844924	1.00[EUR][1000 genomes]
rs4844928	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844935	0.81[AMR][1000 genomes]
rs4844936	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844937	0.84[AMR][1000 genomes]
rs4844938	0.82[AMR][1000 genomes]
rs4844939	0.84[AMR][1000 genomes]
rs4844940	0.82[AMR][1000 genomes]
rs4844941	0.90[AMR][1000 genomes]
rs4844942	0.90[AMR][1000 genomes]
rs4844943	0.93[AMR][1000 genomes]
rs4844944	0.93[AMR][1000 genomes]
rs4844945	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4844946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4844955	0.93[AMR][1000 genomes]
rs72649937	0.86[AMR][1000 genomes]
rs72649938	0.90[AMR][1000 genomes]
rs72649940	0.90[AMR][1000 genomes]
rs72649948	0.93[AMR][1000 genomes]
rs72649949	0.93[AMR][1000 genomes]
rs72649955	0.98[AMR][1000 genomes]
rs72649956	0.93[AMR][1000 genomes]
rs72649959	0.93[AMR][1000 genomes]
rs72649960	0.93[AMR][1000 genomes]
rs72649964	0.90[AMR][1000 genomes]
rs72649967	0.87[AMR][1000 genomes]
rs72649968	0.87[AMR][1000 genomes]
rs7416285	1.00[EUR][1000 genomes]
rs760768	0.84[AMR][1000 genomes]
rs9787400	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv873140	chr1:210068117-210335644	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1821002	chr1:210108473-210291476	ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv873141	chr1:210228131-210296910	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv873142	chr1:210233610-210291121	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv873143	chr1:210233610-210296910	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv873144	chr1:210252522-210347417	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv818800	chr1:210258653-210304319	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3452678	chr1:210284385-210289804	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
10	esv3452679	chr1:210284385-210289804	Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210268400-210287400	Weak transcription	Brain Germinal Matrix	brain
2	chr1:210274200-210290600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:210276600-210285400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:210280000-210290600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:210283000-210298000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:210285200-210285400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:210285200-210285600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links