Variant report

Variant	rs2279701
Chromosome Location	chr8:86210275-86210276
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:86209797..86210360-chr8:87056059..87056917,2	MCF-7	breast:
2	chr8:86209388..86210307-chr8:86375535..86376317,2	K562	blood:
3	chr8:86209311..86210290-chr8:86357968..86358764,3	MCF-7	breast:
4	chr8:86209418..86210324-chr8:87100237..87101601,6	K562	blood:
5	chr8:86209312..86210314-chr8:87045120..87046083,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147613	Chromatin interaction
ENSG00000104267	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs10088120	0.91[JPT][hapmap]
rs10090196	0.92[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs10091582	0.92[ASN][1000 genomes]
rs10095352	0.86[JPT][hapmap]
rs10099251	0.92[ASN][1000 genomes]
rs10100442	0.84[JPT][hapmap]
rs10106970	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10107686	0.86[ASN][1000 genomes]
rs10110461	0.91[ASN][1000 genomes]
rs10111971	0.92[ASN][1000 genomes]
rs1021583	0.92[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10504812	0.82[JPT][hapmap]
rs10504813	0.86[JPT][hapmap]
rs10907474	0.82[JPT][hapmap]
rs11261468	0.81[JPT][hapmap]
rs11261469	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11261471	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11261474	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11985733	0.86[JPT][hapmap]
rs12541299	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12541445	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12543256	0.96[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12544332	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12546106	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12550160	0.92[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12679400	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1303806	0.91[JPT][hapmap]
rs13252971	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs13259399	0.86[JPT][hapmap]
rs13259464	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13269739	0.90[JPT][hapmap]
rs1390711	0.91[JPT][hapmap]
rs1493302	0.87[JPT][hapmap]
rs1496529	0.87[JPT][hapmap]
rs1496530	0.86[JPT][hapmap]
rs1496531	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1496532	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1496533	0.88[ASN][1000 genomes]
rs1532423	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1532424	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1553015	0.91[JPT][hapmap]
rs1553016	0.92[ASN][1000 genomes]
rs1553017	0.91[ASN][1000 genomes]
rs16913681	0.84[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16913721	0.96[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17042	0.83[JPT][hapmap]
rs17740658	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1809819	0.88[ASN][1000 genomes]
rs1845891	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1845892	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1908762	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1995056	0.85[JPT][hapmap]
rs1995057	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1995058	0.91[JPT][hapmap]
rs2006767	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2055077	0.82[JPT][hapmap]
rs20571	0.86[JPT][hapmap]
rs2072696	0.86[JPT][hapmap]
rs2132589	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2132590	0.94[ASN][1000 genomes]
rs2220972	0.81[ASN][1000 genomes]
rs2278459	0.81[JPT][hapmap]
rs2279700	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291786	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2291787	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2307075	0.86[JPT][hapmap]
rs2403083	0.88[CHB][hapmap];0.91[JPT][hapmap]
rs2403085	0.88[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs2403086	0.88[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs2403088	0.81[JPT][hapmap]
rs2403104	0.90[JPT][hapmap]
rs2548281	0.82[JPT][hapmap]
rs2645049	0.82[JPT][hapmap]
rs28374336	0.92[ASN][1000 genomes]
rs28377260	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28439950	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28564613	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28677919	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2896452	0.81[JPT][hapmap]
rs2896454	0.91[JPT][hapmap]
rs3087782	0.82[JPT][hapmap]
rs34103685	0.91[JPT][hapmap]
rs35285802	0.81[EUR][1000 genomes]
rs35558766	0.91[ASN][1000 genomes]
rs3758076	0.87[JPT][hapmap]
rs3779899	0.90[JPT][hapmap]
rs3779901	0.84[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3808538	0.86[JPT][hapmap]
rs3808539	0.91[JPT][hapmap]
rs4150867	0.91[JPT][hapmap]
rs4150868	0.91[JPT][hapmap]
rs4150869	0.85[JPT][hapmap]
rs4150893	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs4150909	0.91[JPT][hapmap]
rs4150942	0.81[JPT][hapmap]
rs4150944	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs4150962	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4150964	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4150974	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4150977	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4566	0.86[JPT][hapmap]
rs4609189	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4617148	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4739698	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4739700	0.86[JPT][hapmap]
rs4740044	0.86[JPT][hapmap]
rs4740045	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4740047	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4740049	0.91[JPT][hapmap]
rs6605610	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6605611	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6605613	0.91[ASN][1000 genomes]
rs6605624	0.80[JPT][hapmap]
rs6988475	0.86[JPT][hapmap]
rs6990449	0.87[JPT][hapmap]
rs6993316	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6993387	0.86[JPT][hapmap]
rs6994113	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6997458	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7001359	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7004871	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7008772	0.86[JPT][hapmap]
rs7011001	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7011926	0.91[JPT][hapmap]
rs7015758	0.91[JPT][hapmap]
rs7016369	0.82[JPT][hapmap]
rs725605	0.82[CHB][hapmap]
rs7818163	0.86[JPT][hapmap]
rs7821629	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7826511	0.84[ASN][1000 genomes]
rs7827175	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7829050	0.91[JPT][hapmap]
rs7829144	0.81[JPT][hapmap]
rs7829240	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7839129	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7841142	0.81[JPT][hapmap]
rs903895	0.91[JPT][hapmap]
rs903896	0.91[JPT][hapmap]
rs903897	0.91[JPT][hapmap]
rs931505	0.83[JPT][hapmap]
rs9329908	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2279701	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs2279701	LRRCC1	cis	Artery Tibial	GTEx
rs2279701	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs2279701	LRRCC1	cis	normal skin	skin_eQTL
rs2279701	LRRCC1	cis	Esophagus Mucosa	GTEx
rs2279701	CA13	cis	Lymphoblastoid	GTEx
rs2279701	CA13	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86197200-86211800	Weak transcription	Fetal Intestine Large	intestine
2	chr8:86197400-86225800	Weak transcription	Fetal Intestine Small	intestine
3	chr8:86208800-86217200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:86209600-86211600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr8:86209800-86210400	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr8:86209800-86211400	Enhancers	Skeletal Muscle Male	skeletal muscle

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