Variant report

Variant	rs903897
Chromosome Location	chr8:86230085-86230086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:86229702..86230332-chr8:86290542..86291598,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133742	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10088120	0.82[JPT][hapmap]
rs10090196	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10091582	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10095352	0.95[JPT][hapmap]
rs10099251	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10107686	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10110461	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10111971	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1014303	0.99[ASN][1000 genomes]
rs1021583	0.87[JPT][hapmap]
rs10504812	0.91[JPT][hapmap]
rs10504813	0.95[JPT][hapmap]
rs10907474	0.91[JPT][hapmap]
rs11261471	0.91[JPT][hapmap]
rs11261472	0.99[ASN][1000 genomes]
rs11261474	0.95[JPT][hapmap]
rs11985733	0.95[JPT][hapmap]
rs11989660	0.99[ASN][1000 genomes]
rs12114575	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12541299	0.81[ASN][1000 genomes]
rs12541445	0.91[JPT][hapmap]
rs12543256	1.00[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs12544332	0.86[JPT][hapmap]
rs12546106	0.86[JPT][hapmap]
rs12550160	0.87[JPT][hapmap]
rs1303806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1303807	0.92[ASN][1000 genomes]
rs13252971	0.95[JPT][hapmap]
rs13259399	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs13269739	0.82[JPT][hapmap]
rs1390711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1493302	0.95[JPT][hapmap]
rs1496529	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1496530	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1496531	0.86[JPT][hapmap]
rs1496532	0.86[JPT][hapmap]
rs1496533	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1532423	0.91[JPT][hapmap]
rs1532424	0.95[JPT][hapmap]
rs1553015	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1553016	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1553017	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16913681	0.87[JPT][hapmap]
rs16913721	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs17042	0.91[JPT][hapmap]
rs17740658	0.86[JPT][hapmap]
rs1809819	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1908762	0.82[JPT][hapmap]
rs1995056	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1995057	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1995058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2006767	0.95[JPT][hapmap]
rs2055077	0.91[JPT][hapmap]
rs20571	0.95[JPT][hapmap]
rs2072696	0.95[JPT][hapmap]
rs2132589	0.86[JPT][hapmap]
rs2132590	0.89[EUR][1000 genomes]
rs2278459	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs2279701	0.91[JPT][hapmap]
rs2291786	0.86[JPT][hapmap]
rs2291787	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2307075	0.95[JPT][hapmap]
rs2403083	0.82[JPT][hapmap]
rs2403085	0.83[JPT][hapmap]
rs2403086	0.82[JPT][hapmap]
rs2403088	0.91[JPT][hapmap]
rs2403104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2548281	0.91[JPT][hapmap]
rs2645049	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs28374336	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28494527	0.86[ASN][1000 genomes]
rs28677919	0.81[ASN][1000 genomes]
rs2896452	0.91[JPT][hapmap]
rs2896454	0.82[JPT][hapmap]
rs3087782	0.91[JPT][hapmap]
rs34103685	0.82[JPT][hapmap]
rs35285802	0.88[ASN][1000 genomes]
rs35558766	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3758076	0.95[JPT][hapmap]
rs3779899	0.81[JPT][hapmap]
rs3779901	0.87[JPT][hapmap]
rs3808538	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs3808539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150867	0.83[JPT][hapmap]
rs4150868	0.82[JPT][hapmap]
rs4150869	0.81[JPT][hapmap]
rs4150893	0.82[JPT][hapmap]
rs4150909	0.82[JPT][hapmap]
rs4150942	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4150944	0.82[JPT][hapmap]
rs4150964	0.86[JPT][hapmap]
rs4150974	0.86[JPT][hapmap]
rs4150977	0.86[JPT][hapmap]
rs4566	0.95[JPT][hapmap]
rs4609189	0.87[JPT][hapmap]
rs4739700	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4739702	0.99[ASN][1000 genomes]
rs4740043	0.86[JPT][hapmap]
rs4740044	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4740045	0.86[JPT][hapmap]
rs4740048	0.97[ASN][1000 genomes]
rs4740049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs62527225	0.82[ASN][1000 genomes]
rs6605610	0.87[JPT][hapmap]
rs6605611	0.86[JPT][hapmap]
rs6605613	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6605624	0.90[JPT][hapmap]
rs67573812	0.82[ASN][1000 genomes]
rs6987641	0.83[ASN][1000 genomes]
rs6988475	0.95[JPT][hapmap]
rs6990449	0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs6990452	0.82[ASN][1000 genomes]
rs6993387	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6994113	0.86[JPT][hapmap]
rs6997458	0.91[JPT][hapmap]
rs7001359	0.91[JPT][hapmap]
rs7004871	0.92[ASN][1000 genomes]
rs7008772	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7011926	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7015758	0.83[JPT][hapmap]
rs7016369	0.91[JPT][hapmap]
rs725605	0.86[JPT][hapmap]
rs7818163	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7826511	0.93[EUR][1000 genomes]
rs7827175	0.86[JPT][hapmap]
rs7829050	0.83[JPT][hapmap]
rs7833737	0.93[ASN][1000 genomes]
rs7835303	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7835882	0.83[ASN][1000 genomes]
rs7837275	0.92[ASN][1000 genomes]
rs7841142	0.91[JPT][hapmap]
rs903895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs903896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs931505	0.91[JPT][hapmap]
rs9969643	0.95[JPT][hapmap]
rs9987281	0.95[JPT][hapmap]

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	nsv1018483	chr8:86142258-86547831	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024759	chr8:86162507-86361533	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv539659	chr8:86162507-86361533	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv971674	chr8:86187966-86338484	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv2761442	chr8:86201657-86230641	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs903897	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs903897	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs903897	CA13	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86228400-86230800	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr8:86228800-86230200	Enhancers	H1 Cell Line	embryonic stem cell
3	chr8:86228800-86230600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr8:86229000-86230200	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr8:86229000-86230800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr8:86229000-86231000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr8:86229200-86230200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr8:86229200-86231000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr8:86229600-86230200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr8:86229800-86230600	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr8:86230000-86230800	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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