Variant report

Variant	rs1540821
Chromosome Location	chr2:168175848-168175849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 142 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10186558	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10189334	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10192896	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1048981	0.84[CEU][hapmap];0.81[GIH][hapmap]
rs10497321	0.82[CEU][hapmap]
rs10803821	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10803822	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10930264	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10930265	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10930268	0.82[EUR][1000 genomes]
rs10930270	0.82[EUR][1000 genomes]
rs12105767	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12692859	0.82[EUR][1000 genomes]
rs1357598	0.83[AFR][1000 genomes]
rs1357599	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1357605	0.81[EUR][1000 genomes]
rs1382318	0.82[EUR][1000 genomes]
rs1403894	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1403897	0.82[EUR][1000 genomes]
rs1403898	0.82[EUR][1000 genomes]
rs1403899	0.82[EUR][1000 genomes]
rs1403900	0.91[EUR][1000 genomes]
rs1403901	0.91[EUR][1000 genomes]
rs1478384	0.82[EUR][1000 genomes]
rs1478385	0.82[EUR][1000 genomes]
rs1479587	0.81[EUR][1000 genomes]
rs1479591	0.81[EUR][1000 genomes]
rs1523878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1523882	0.82[EUR][1000 genomes]
rs1540820	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1540822	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1568747	0.82[EUR][1000 genomes]
rs1581484	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1581485	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1589728	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1608518	0.81[AMR][1000 genomes]
rs1608519	0.82[EUR][1000 genomes]
rs1608520	0.82[EUR][1000 genomes]
rs16853227	0.82[CEU][hapmap]
rs16853282	0.82[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap]
rs16853285	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs16853291	0.82[CEU][hapmap]
rs16853296	0.82[CEU][hapmap]
rs16853305	0.82[CEU][hapmap]
rs16853306	0.91[CEU][hapmap]
rs16853309	0.82[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs16853328	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs16853330	0.91[CEU][hapmap]
rs16853331	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs16853337	0.82[CEU][hapmap]
rs16853344	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs16853346	0.82[EUR][1000 genomes]
rs16853348	0.81[EUR][1000 genomes]
rs16853353	0.81[EUR][1000 genomes]
rs16853360	0.81[EUR][1000 genomes]
rs16853370	0.82[EUR][1000 genomes]
rs1851758	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1851759	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1851760	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1916742	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1916746	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1916747	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1916748	0.82[EUR][1000 genomes]
rs1916749	0.82[EUR][1000 genomes]
rs1916750	0.82[EUR][1000 genomes]
rs1916751	0.82[EUR][1000 genomes]
rs1996949	0.82[EUR][1000 genomes]
rs2103098	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2140501	0.86[EUR][1000 genomes]
rs2177441	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2177442	0.84[EUR][1000 genomes]
rs2250619	0.82[EUR][1000 genomes]
rs2617368	0.91[EUR][1000 genomes]
rs2617386	0.82[EUR][1000 genomes]
rs2617388	0.82[EUR][1000 genomes]
rs2617391	0.82[EUR][1000 genomes]
rs2617393	0.82[EUR][1000 genomes]
rs2617394	0.82[EUR][1000 genomes]
rs2617398	0.82[EUR][1000 genomes]
rs2617399	0.82[EUR][1000 genomes]
rs2689820	0.82[EUR][1000 genomes]
rs2689823	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2689825	0.82[EUR][1000 genomes]
rs2689826	0.82[EUR][1000 genomes]
rs2689827	0.82[EUR][1000 genomes]
rs2689828	0.82[EUR][1000 genomes]
rs2689832	0.82[EUR][1000 genomes]
rs2689833	0.82[EUR][1000 genomes]
rs2689842	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2927600	0.93[EUR][1000 genomes]
rs2949009	0.82[EUR][1000 genomes]
rs2949010	0.82[EUR][1000 genomes]
rs3749004	0.82[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs3749006	0.91[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs4538166	0.92[EUR][1000 genomes]
rs4667949	0.82[EUR][1000 genomes]
rs57797869	0.92[EUR][1000 genomes]
rs58013803	0.92[EUR][1000 genomes]
rs60102532	0.92[EUR][1000 genomes]
rs61529696	0.92[EUR][1000 genomes]
rs6432987	0.82[CEU][hapmap]
rs6715974	0.81[EUR][1000 genomes]
rs6716354	0.81[EUR][1000 genomes]
rs6726067	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6731860	0.81[EUR][1000 genomes]
rs6735992	0.81[EUR][1000 genomes]
rs6743941	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6744215	0.81[EUR][1000 genomes]
rs6746887	0.84[EUR][1000 genomes]
rs6747157	0.81[EUR][1000 genomes]
rs6747227	0.91[CEU][hapmap]
rs6749022	0.81[EUR][1000 genomes]
rs6749144	0.81[EUR][1000 genomes]
rs6759681	0.81[CEU][hapmap]
rs73012072	0.81[EUR][1000 genomes]
rs73972228	0.92[EUR][1000 genomes]
rs73972230	0.92[EUR][1000 genomes]
rs7573953	0.91[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs7576187	0.82[EUR][1000 genomes]
rs7576938	0.82[CEU][hapmap]
rs7578175	0.81[EUR][1000 genomes]
rs7580183	0.82[CEU][hapmap]
rs7581012	0.82[CEU][hapmap]
rs7581190	0.91[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap]
rs7593641	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7594496	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7600424	0.82[CEU][hapmap]
rs7602109	0.91[CEU][hapmap]
rs7604377	0.81[EUR][1000 genomes]
rs7607246	0.82[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap]
rs899185	0.82[EUR][1000 genomes]
rs922536	0.82[CEU][hapmap]
rs922537	0.82[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap]
rs9287881	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs940315	0.82[EUR][1000 genomes]
rs9751663	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9751666	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875377	chr2:168084857-168203116	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv875378	chr2:168107491-168297961	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv3364733	chr2:168109919-168302141	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv1008704	chr2:168153525-168196371	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2763488	chr2:168163136-168181440	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:168174000-168176000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
2	chr2:168174200-168179400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:168174400-168176000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:168174800-168176200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
5	chr2:168174800-168176400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
6	chr2:168174800-168176600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
7	chr2:168175200-168176000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:168175600-168176400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr2:168175800-168178000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:168175800-168187600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links