Variant report

Variant	rs6545381
Chromosome Location	chr2:54253251-54253252
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54247772..54249970-chr2:54252060..54254811,2	MCF-7	breast:

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10084374	0.92[ASN][1000 genomes]
rs10167891	0.89[ASN][1000 genomes]
rs10181999	0.94[ASN][1000 genomes]
rs10183655	0.86[CHB][hapmap]
rs10186566	0.85[ASN][1000 genomes]
rs10496028	0.85[AFR][1000 genomes]
rs11674724	0.89[ASN][1000 genomes]
rs11676462	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11683741	0.80[AMR][1000 genomes]
rs11689025	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11890838	0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs11893270	0.94[ASN][1000 genomes]
rs11896815	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11898855	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13394278	0.87[ASN][1000 genomes]
rs1477258	0.86[ASN][1000 genomes]
rs17039547	0.83[CEU][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap]
rs17045452	0.91[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs17045474	0.92[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17045488	0.92[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2112122	0.89[ASN][1000 genomes]
rs2287643	0.83[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes]
rs2302879	0.82[AMR][1000 genomes]
rs2357896	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28653587	0.87[ASN][1000 genomes]
rs28851028	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2909459	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34498089	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs34773403	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3731967	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs4671742	0.80[ASN][1000 genomes]
rs4671746	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671747	0.85[ASN][1000 genomes]
rs4671861	0.80[AMR][1000 genomes]
rs55649409	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55692047	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55705819	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs56193146	0.85[AFR][1000 genomes]
rs56302494	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62137964	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs62137976	0.80[AMR][1000 genomes]
rs62137980	0.82[AMR][1000 genomes]
rs62139336	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62140990	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62141002	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6545377	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6545380	0.85[ASN][1000 genomes]
rs6545386	0.82[AMR][1000 genomes]
rs6711105	0.92[ASN][1000 genomes]
rs6711217	0.89[ASN][1000 genomes]
rs6714450	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6715488	0.88[ASN][1000 genomes]
rs6721970	0.82[CEU][hapmap];0.92[YRI][hapmap]
rs6743455	0.94[ASN][1000 genomes]
rs6746965	0.92[CHB][hapmap];0.87[ASN][1000 genomes]
rs6748976	0.90[ASN][1000 genomes]
rs6748997	0.88[ASN][1000 genomes]
rs698855	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs698857	0.83[AMR][1000 genomes]
rs72799298	0.90[ASN][1000 genomes]
rs72904908	0.82[ASN][1000 genomes]
rs7559384	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7559947	0.83[ASN][1000 genomes]
rs7564912	0.87[ASN][1000 genomes]
rs7565453	0.82[AMR][1000 genomes]
rs7573551	0.80[AFR][1000 genomes]
rs7576901	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7590819	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7591431	0.87[ASN][1000 genomes]
rs805310	0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs805312	0.82[AMR][1000 genomes]
rs805313	0.85[AMR][1000 genomes]
rs805316	0.91[YRI][hapmap]
rs805319	0.82[AMR][1000 genomes]
rs805321	0.87[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes]
rs805323	0.82[AMR][1000 genomes]
rs805328	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs805329	0.81[AMR][1000 genomes]
rs805338	1.00[YRI][hapmap]
rs805344	0.81[AMR][1000 genomes]
rs805346	0.82[AMR][1000 genomes]
rs805347	0.82[AMR][1000 genomes]
rs805348	0.81[AMR][1000 genomes]
rs805351	0.87[CEU][hapmap];0.83[CHB][hapmap];0.86[AMR][1000 genomes]
rs805352	0.87[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes]
rs805354	0.86[AMR][1000 genomes]
rs805355	0.86[AMR][1000 genomes]
rs805356	0.86[AMR][1000 genomes]
rs805357	0.86[AMR][1000 genomes]
rs805362	0.86[AMR][1000 genomes]
rs805363	0.82[AMR][1000 genomes]
rs805365	0.87[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes]
rs805386	0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes]
rs805388	0.81[AMR][1000 genomes]
rs805390	0.81[AMR][1000 genomes]
rs805394	0.82[AMR][1000 genomes]
rs805397	0.85[AMR][1000 genomes]
rs805399	0.82[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes]
rs805400	0.83[AMR][1000 genomes]
rs805401	0.82[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes]
rs805404	0.87[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes]
rs805406	0.83[AMR][1000 genomes]
rs805407	0.83[AMR][1000 genomes]
rs805408	0.87[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes]
rs805409	0.82[AMR][1000 genomes]
rs805411	0.83[AMR][1000 genomes]
rs805414	0.83[AMR][1000 genomes]
rs805415	0.82[AMR][1000 genomes]
rs805419	0.82[AMR][1000 genomes]
rs805420	0.82[AMR][1000 genomes]
rs805425	0.81[AMR][1000 genomes]
rs805426	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs805446	1.00[YRI][hapmap]
rs805449	1.00[YRI][hapmap]
rs809282	0.83[AMR][1000 genomes]
rs9631059	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv963232	chr2:54249008-54261054	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6545381	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54240200-54257000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr2:54243400-54254200	Weak transcription	Fetal Stomach	stomach
3	chr2:54243800-54255400	Weak transcription	HepG2	liver
4	chr2:54243800-54268000	Weak transcription	Osteobl	bone
5	chr2:54243800-54268400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:54243800-54269800	Weak transcription	Brain Anterior Caudate	brain
7	chr2:54244400-54254200	Weak transcription	Ovary	ovary
8	chr2:54246800-54275200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:54248400-54254600	Weak transcription	Liver	Liver
10	chr2:54248400-54256800	Weak transcription	Pancreas	Pancrea
11	chr2:54248400-54257400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:54248600-54256800	Weak transcription	Psoas Muscle	Psoas
13	chr2:54248600-54278000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
15	chr2:54248800-54275600	Weak transcription	Primary B cells from cord blood	blood
16	chr2:54250000-54257600	Weak transcription	Gastric	stomach
17	chr2:54250000-54257600	Weak transcription	Left Ventricle	heart
18	chr2:54251600-54263800	Weak transcription	Primary T cells from cord blood	blood
19	chr2:54252600-54258000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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