Variant report

Variant	rs10084374
Chromosome Location	chr2:54249312-54249313
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	chr2:54247772..54249970-chr2:54252060..54254811,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10084355	0.82[EUR][1000 genomes]
rs10167891	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10168293	0.82[EUR][1000 genomes]
rs10181999	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10183655	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10186566	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11674724	0.88[ASN][1000 genomes]
rs11676462	0.84[ASN][1000 genomes]
rs11694711	0.82[EUR][1000 genomes]
rs11884699	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11890838	0.89[ASN][1000 genomes]
rs11893270	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11896815	0.83[ASN][1000 genomes]
rs11898855	0.93[ASN][1000 genomes]
rs12713253	0.81[EUR][1000 genomes]
rs13394278	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1421617	0.81[EUR][1000 genomes]
rs1477258	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17045474	0.88[ASN][1000 genomes]
rs17045488	0.85[ASN][1000 genomes]
rs17268179	0.81[EUR][1000 genomes]
rs2112121	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2112122	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2357896	0.83[ASN][1000 genomes]
rs28653587	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28851028	0.83[ASN][1000 genomes]
rs3731967	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4671742	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4671746	0.87[ASN][1000 genomes]
rs4671747	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55649409	0.83[ASN][1000 genomes]
rs55692047	0.86[ASN][1000 genomes]
rs56302494	0.86[ASN][1000 genomes]
rs6545377	0.85[ASN][1000 genomes]
rs6545380	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545381	0.92[ASN][1000 genomes]
rs66773232	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6711105	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6711217	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6714450	0.92[ASN][1000 genomes]
rs6715488	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742042	0.83[EUR][1000 genomes]
rs6743455	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6746965	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6748976	0.87[ASN][1000 genomes]
rs6748997	0.83[ASN][1000 genomes]
rs6749817	0.82[EUR][1000 genomes]
rs72799298	0.87[ASN][1000 genomes]
rs72904908	0.87[ASN][1000 genomes]
rs7559380	0.80[EUR][1000 genomes]
rs7559384	0.91[ASN][1000 genomes]
rs7564912	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7591431	0.87[ASN][1000 genomes]
rs7597189	0.81[ASN][1000 genomes]
rs9631059	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10084374	PSME4	Cis_1M	lymphoblastoid	RTeQTL
rs10084374	ACYP2	cis	Esophagus Mucosa	GTEx
rs10084374	ACYP2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54213600-54249800	Weak transcription	Left Ventricle	heart
2	chr2:54240200-54257000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:54242200-54251800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr2:54243400-54254200	Weak transcription	Fetal Stomach	stomach
5	chr2:54243800-54255400	Weak transcription	HepG2	liver
6	chr2:54243800-54268000	Weak transcription	Osteobl	bone
7	chr2:54243800-54268400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:54243800-54269800	Weak transcription	Brain Anterior Caudate	brain
9	chr2:54244400-54254200	Weak transcription	Ovary	ovary
10	chr2:54246600-54249600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:54246800-54275200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:54247200-54250000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:54247600-54249400	ZNF genes & repeats	Primary T cells from cord blood	blood
14	chr2:54248200-54250200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:54248400-54249800	Weak transcription	Gastric	stomach
16	chr2:54248400-54254600	Weak transcription	Liver	Liver
17	chr2:54248400-54256800	Weak transcription	Pancreas	Pancrea
18	chr2:54248400-54257400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:54248600-54252000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:54248600-54256800	Weak transcription	Psoas Muscle	Psoas
21	chr2:54248600-54278000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
23	chr2:54248800-54275600	Weak transcription	Primary B cells from cord blood	blood

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