Variant report

Variant	rs4671747
Chromosome Location	chr2:54229818-54229819
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	chr2:54209836..54212670-chr2:54227485..54229972,3	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10084374	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10167891	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10168293	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10181999	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10183655	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10186566	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11674724	0.93[ASN][1000 genomes]
rs11683741	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11689025	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11694711	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11884699	0.83[ASN][1000 genomes]
rs11890838	0.80[ASN][1000 genomes]
rs11893270	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11898855	0.84[ASN][1000 genomes]
rs13394278	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1477258	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17045452	0.85[ASN][1000 genomes]
rs2112122	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28653587	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28851028	0.88[ASN][1000 genomes]
rs2909459	0.83[ASN][1000 genomes]
rs2949815	0.81[ASN][1000 genomes]
rs3731967	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671742	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671746	0.95[ASN][1000 genomes]
rs55692047	0.92[ASN][1000 genomes]
rs56302494	0.94[ASN][1000 genomes]
rs62139336	0.85[ASN][1000 genomes]
rs6545377	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6545380	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545381	0.85[ASN][1000 genomes]
rs66773232	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6711105	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6711217	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6714450	0.84[ASN][1000 genomes]
rs6715488	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6742042	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6743455	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6746965	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6748976	0.91[ASN][1000 genomes]
rs6748997	0.94[ASN][1000 genomes]
rs72799298	0.91[ASN][1000 genomes]
rs72904908	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7559384	0.82[ASN][1000 genomes]
rs7559947	0.85[ASN][1000 genomes]
rs7564912	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7591431	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7597188	0.84[ASN][1000 genomes]
rs7597189	0.83[ASN][1000 genomes]
rs805310	0.83[ASN][1000 genomes]
rs805344	0.83[ASN][1000 genomes]
rs805416	0.82[AMR][1000 genomes]
rs9631059	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4671747	PSME4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54208400-54248200	Weak transcription	Lung	lung
2	chr2:54211400-54243000	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:54213600-54249800	Weak transcription	Left Ventricle	heart
4	chr2:54215000-54242800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:54216400-54242000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:54217000-54236600	Weak transcription	Brain Angular Gyrus	brain
7	chr2:54217000-54236800	Weak transcription	Brain Anterior Caudate	brain
8	chr2:54217000-54248200	Weak transcription	Gastric	stomach
9	chr2:54217200-54233800	Weak transcription	HepG2	liver
10	chr2:54217200-54239600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:54224400-54239600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:54226000-54231000	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:54226000-54240000	Weak transcription	Primary B cells from cord blood	blood
14	chr2:54226200-54239600	Weak transcription	Adipose Nuclei	Adipose
15	chr2:54226600-54243000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:54226800-54236800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:54226800-54239000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:54226800-54239200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr2:54228200-54236600	Weak transcription	Primary T cells from cord blood	blood
20	chr2:54228400-54239600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:54228800-54243400	Weak transcription	Fetal Lung	lung
22	chr2:54229000-54243000	Weak transcription	Right Atrium	heart
23	chr2:54229200-54245800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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