Variant report

Variant	rs12541445
Chromosome Location	chr8:86201809-86201810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:86176240..86178800-chr8:86200957..86202565,2	MCF-7	breast:
2	chr8:86131309..86134784-chr8:86200962..86204075,3	MCF-7	breast:
3	chr8:86201309..86204247-chr8:86206649..86208335,2	K562	blood:
4	chr8:86059423..86060332-chr8:86201778..86202999,3	MCF-7	breast:
5	chr8:86132574..86133932-chr8:86200875..86203499,32	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176731	Chromatin interaction
ENSG00000185015	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs10088120	0.91[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs10090196	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs10091582	0.94[ASN][1000 genomes]
rs10095352	0.86[JPT][hapmap]
rs10099251	0.94[ASN][1000 genomes]
rs10100442	0.84[JPT][hapmap];0.88[TSI][hapmap]
rs10106970	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10107686	0.88[ASN][1000 genomes]
rs10110461	0.93[ASN][1000 genomes]
rs10111971	0.94[ASN][1000 genomes]
rs1021583	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10504812	0.82[JPT][hapmap]
rs10504813	0.86[JPT][hapmap]
rs10907474	0.82[JPT][hapmap]
rs11261468	0.81[JPT][hapmap];0.80[MEX][hapmap]
rs11261469	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11261471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11261474	0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs11985733	0.86[JPT][hapmap]
rs12541299	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12543256	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12544332	0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12546106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12550160	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12679400	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1303806	0.91[JPT][hapmap]
rs13252971	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs13259399	0.83[CHB][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap]
rs13259464	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13269739	0.90[JPT][hapmap]
rs1390711	0.91[JPT][hapmap]
rs1493302	0.86[JPT][hapmap]
rs1496529	0.86[JPT][hapmap]
rs1496530	0.86[JPT][hapmap]
rs1496531	0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1496532	0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1496533	0.90[ASN][1000 genomes]
rs1532423	0.82[JPT][hapmap]
rs1532424	0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs1553015	0.91[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs1553016	0.94[ASN][1000 genomes]
rs1553017	0.93[ASN][1000 genomes]
rs16913681	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16913721	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs17042	0.82[JPT][hapmap]
rs17740658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1809819	0.90[ASN][1000 genomes]
rs1845891	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1845892	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1908762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1995056	0.85[JPT][hapmap];0.86[TSI][hapmap]
rs1995057	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1995058	0.91[JPT][hapmap]
rs2006767	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2055077	0.82[JPT][hapmap]
rs20571	0.86[JPT][hapmap]
rs2072696	0.85[JPT][hapmap]
rs2132589	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2132590	0.96[ASN][1000 genomes]
rs2220972	0.82[ASN][1000 genomes]
rs2278459	0.81[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs2279700	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279701	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291787	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2307075	0.86[JPT][hapmap]
rs2403083	0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2403084	0.80[ASN][1000 genomes]
rs2403085	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2403086	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2403088	0.81[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs2403104	0.90[JPT][hapmap];0.86[TSI][hapmap]
rs2548281	0.82[JPT][hapmap]
rs2645049	0.82[JPT][hapmap]
rs28374336	0.94[ASN][1000 genomes]
rs28377260	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28439950	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28564613	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28677919	0.86[EUR][1000 genomes]
rs2896452	0.81[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs2896454	0.91[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs3087782	0.82[JPT][hapmap]
rs34103685	0.91[JPT][hapmap];1.00[MEX][hapmap]
rs35558766	0.93[ASN][1000 genomes]
rs3758076	0.86[JPT][hapmap]
rs3779899	0.90[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs3779901	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3808538	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs3808539	0.91[JPT][hapmap]
rs4150867	0.91[JPT][hapmap]
rs4150868	0.90[JPT][hapmap]
rs4150869	0.85[JPT][hapmap]
rs4150893	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap]
rs4150909	0.83[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs4150942	0.81[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap]
rs4150944	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4150962	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4150964	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4150974	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4150977	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4566	0.86[JPT][hapmap]
rs4609189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4617148	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4739698	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4739700	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]
rs4740044	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4740045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4740047	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4740048	0.80[ASN][1000 genomes]
rs4740049	0.91[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs6605610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6605611	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6605613	0.93[ASN][1000 genomes]
rs6605624	0.80[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs6988475	0.86[JPT][hapmap]
rs6990449	0.86[JPT][hapmap]
rs6993316	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6993387	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6994113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6997458	0.82[JPT][hapmap]
rs7001359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7004871	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7008772	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7011001	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7011926	0.91[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs7015758	0.91[JPT][hapmap]
rs7016369	0.82[JPT][hapmap]
rs7818163	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs7821629	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7826511	0.86[ASN][1000 genomes]
rs7827175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7829050	0.91[JPT][hapmap]
rs7829144	0.81[JPT][hapmap];0.88[MEX][hapmap]
rs7829240	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7837275	0.81[ASN][1000 genomes]
rs7839129	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7841142	0.81[JPT][hapmap]
rs903895	0.91[JPT][hapmap]
rs903896	0.91[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs903897	0.91[JPT][hapmap]
rs931505	0.82[JPT][hapmap]
rs9329908	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9969643	0.86[JPT][hapmap]
rs9987281	0.86[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12541445	LRRCC1	cis	parietal	SCAN
rs12541445	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs12541445	LRRCC1	cis	Esophagus Mucosa	GTEx
rs12541445	CA13	cis	lymphoblastoid	seeQTL
rs12541445	C8orf59	cis	cerebellum	SCAN
rs12541445	CA13	cis	cerebellum	SCAN
rs12541445	C8orf59	cis	parietal	SCAN
rs12541445	LRRCC1	cis	Artery Tibial	GTEx
rs12541445	LRRCC1	cis	cerebellum	SCAN
rs12541445	C8orf59	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86170800-86204400	Weak transcription	Ovary	ovary
2	chr8:86190200-86203600	Weak transcription	Fetal Stomach	stomach
3	chr8:86190200-86208400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr8:86190200-86209600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr8:86190200-86209600	Weak transcription	Gastric	stomach
6	chr8:86191200-86208400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr8:86196800-86202400	Weak transcription	Fetal Lung	lung
8	chr8:86197200-86211800	Weak transcription	Fetal Intestine Large	intestine
9	chr8:86197400-86225800	Weak transcription	Fetal Intestine Small	intestine
10	chr8:86199800-86205600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr8:86201200-86202200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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