Variant report

Variant	rs10204628
Chromosome Location	chr2:191488854-191488855
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10931455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10931459	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10931460	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10931464	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11673788	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs11675051	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11677333	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11685221	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11686226	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11891641	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13005335	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2159821	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2159822	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34101385	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34109383	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34703964	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34751744	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35954637	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3934784	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4324341	0.85[ASN][1000 genomes]
rs4343493	0.88[JPT][hapmap]
rs4384819	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4384820	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4597559	0.88[JPT][hapmap]
rs4638823	0.88[JPT][hapmap]
rs55784091	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55788736	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55884870	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55901912	0.85[ASN][1000 genomes]
rs56094872	0.83[ASN][1000 genomes]
rs56337518	0.85[ASN][1000 genomes]
rs61730953	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61743479	0.81[EUR][1000 genomes]
rs62181024	0.83[ASN][1000 genomes]
rs62181026	0.83[ASN][1000 genomes]
rs62181027	0.83[ASN][1000 genomes]
rs62181031	0.81[ASN][1000 genomes]
rs62181032	0.85[ASN][1000 genomes]
rs62181033	0.85[ASN][1000 genomes]
rs62181036	0.83[ASN][1000 genomes]
rs62181053	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62181057	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182860	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182861	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182862	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182863	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182864	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182892	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62182893	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6434404	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6714829	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6719656	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6727054	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6742904	1.00[YRI][hapmap]
rs6756354	0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs6757698	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs72907168	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72911128	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7573621	0.83[ASN][1000 genomes]
rs7574871	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7721	0.82[ASW][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834492	chr2:191438864-191646621	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10204628	FLJ20160	Cis_1M	lymphoblastoid	RTeQTL
rs10204628	HIBCH	cis	lymphoblastoid	seeQTL
rs10204628	ZC3H15	cis	cerebellum	SCAN
rs10204628	INPP1	cis	cerebellum	SCAN
rs10204628	MFSD6	cis	lymphoblastoid	seeQTL
rs10204628	HIBCH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191456600-191491800	Weak transcription	Aorta	Aorta
2	chr2:191475400-191492400	Weak transcription	Fetal Brain Male	brain
3	chr2:191477000-191491400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:191486800-191492400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:191488800-191489200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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