Variant report

Variant	rs12759119
Chromosome Location	chr1:225441678-225441679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 161 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs1067206	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1067207	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10799296	0.96[EUR][1000 genomes]
rs10915791	0.96[EUR][1000 genomes]
rs10915797	0.96[EUR][1000 genomes]
rs10915798	0.96[EUR][1000 genomes]
rs10915802	0.96[EUR][1000 genomes]
rs10915803	0.96[EUR][1000 genomes]
rs10915806	0.99[EUR][1000 genomes]
rs11577306	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11578729	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11580638	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11582482	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11583802	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11584486	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11585032	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11585124	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11586783	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11587822	0.89[CHB][hapmap]
rs12064555	0.96[EUR][1000 genomes]
rs12068189	0.96[EUR][1000 genomes]
rs12068193	0.96[EUR][1000 genomes]
rs12077485	0.96[EUR][1000 genomes]
rs12077966	0.96[EUR][1000 genomes]
rs12090119	0.96[EUR][1000 genomes]
rs12097990	0.96[EUR][1000 genomes]
rs12402229	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12403292	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12403752	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12403778	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12406388	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12408302	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12408521	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs12410126	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12410491	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12411172	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12411174	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12728007	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12729289	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12733373	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12733733	0.96[EUR][1000 genomes]
rs12736406	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12740067	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12740354	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12754116	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12754197	0.88[CEU][hapmap]
rs12754230	0.96[EUR][1000 genomes]
rs12758681	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12758819	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1466468	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1480101	1.00[CEU][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes]
rs1480107	0.96[EUR][1000 genomes]
rs1553447	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs1604777	0.89[CHB][hapmap];0.84[CHD][hapmap]
rs16844054	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16844408	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16844602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16844689	0.88[CEU][hapmap];0.83[MKK][hapmap]
rs1842332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1847906	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1847907	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2035302	0.96[EUR][1000 genomes]
rs34051059	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34115920	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34248528	0.96[EUR][1000 genomes]
rs34256167	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34304596	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34305765	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34436845	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34468096	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34517951	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34524645	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34530213	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34737903	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34764920	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34766551	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34778535	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34937935	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35150136	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35161243	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35181350	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35352581	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35553993	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35852721	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35948433	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36053633	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4319288	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4623662	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653413	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653607	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653608	0.96[EUR][1000 genomes]
rs4653610	0.96[EUR][1000 genomes]
rs4653614	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4653628	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs55680010	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55738724	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55770610	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56280792	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56332582	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57650955	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs581675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs582720	0.83[JPT][hapmap]
rs583098	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs584720	0.84[JPT][hapmap]
rs59493468	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs599355	0.84[JPT][hapmap]
rs608979	0.84[JPT][hapmap]
rs61849836	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61851475	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61851476	0.89[EUR][1000 genomes]
rs61851478	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61851479	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61851481	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61851487	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61851489	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61851518	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61851519	0.96[EUR][1000 genomes]
rs61851520	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs621210	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs622158	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs633544	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs633994	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs634342	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs634895	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs635851	0.84[JPT][hapmap]
rs638371	0.84[JPT][hapmap]
rs638672	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs655529	0.84[JPT][hapmap]
rs661753	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6666735	0.95[EUR][1000 genomes]
rs669326	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6693785	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs672951	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs674025	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs675571	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs686493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs712060	0.84[JPT][hapmap]
rs712061	0.84[JPT][hapmap]
rs71646708	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72748625	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7536245	1.00[CEU][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes]
rs7541259	0.96[EUR][1000 genomes]
rs7555756	0.96[EUR][1000 genomes]
rs9887766	0.96[EUR][1000 genomes]
rs9887975	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998899	chr1:225210813-225496353	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv468205	chr1:225304971-225476025	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv549264	chr1:225304971-225476025	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv945672	chr1:225339532-225561349	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv873226	chr1:225347689-225555602	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv832703	chr1:225375953-225520216	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1014968	chr1:225389490-225459008	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
8	nsv1005481	chr1:225389490-225462887	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
9	nsv997904	chr1:225389490-225466637	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1002430	chr1:225389490-225471683	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv2762171	chr1:225390933-225463772	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
12	nsv549265	chr1:225395959-225462346	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
13	esv1805729	chr1:225404951-225526778	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv2757774	chr1:225404951-225526778	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv2759002	chr1:225404951-225526778	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv428312	chr1:225404951-225526778	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12759119	LBR	cis	parietal	SCAN
rs12759119	ACBD3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225441200-225442400	Enhancers	NH-A	brain
2	chr1:225441400-225442000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:225441400-225442200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:225441400-225442200	Enhancers	NHEK	skin
5	chr1:225441400-225442600	Enhancers	HMEC	breast
6	chr1:225441600-225442000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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