Variant report

Variant	rs17045474
Chromosome Location	chr2:54274973-54274974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr2:54274949-54275120	K562	blood:	n/a	n/a
2	EP300	chr2:54274734-54275085	K562	blood:	n/a	n/a
3	JUN	chr2:54274891-54275196	K562	blood:	n/a	chr2:54275014-54275021 chr2:54275013-54275021
4	NR2F2	chr2:54274851-54275208	K562	blood:	n/a	n/a
5	JUND	chr2:54274882-54275108	K562	blood:	n/a	chr2:54275014-54275021 chr2:54275013-54275021
6	NR2F2	chr2:54274764-54275306	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54274074..54275911-chr2:54277300..54280127,2	MCF-7	breast:

Variant related genes	Relation type
HMGB1P31	TF binding region
ENSG00000233266	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10084374	0.88[ASN][1000 genomes]
rs10167891	0.81[ASN][1000 genomes]
rs10181999	0.91[ASN][1000 genomes]
rs10183655	0.82[CHB][hapmap]
rs10186566	0.82[ASN][1000 genomes]
rs10496028	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11674724	0.85[ASN][1000 genomes]
rs11676462	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11683654	0.84[CEU][hapmap]
rs11890838	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs11893270	0.87[ASN][1000 genomes]
rs11896815	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11898855	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17039547	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17045452	0.86[CHB][hapmap]
rs17045488	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1877908	0.83[JPT][hapmap]
rs2112122	0.87[ASN][1000 genomes]
rs2287643	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2357896	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28653587	0.80[ASN][1000 genomes]
rs2909459	0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap]
rs34498089	0.86[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34773403	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3731967	0.82[CHB][hapmap]
rs4671746	0.84[ASN][1000 genomes]
rs4671861	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55649409	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55692047	0.84[ASN][1000 genomes]
rs55705819	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56193146	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56302494	0.83[ASN][1000 genomes]
rs62137964	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62137976	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62137980	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62140990	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62141002	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545377	0.81[ASN][1000 genomes]
rs6545380	0.83[ASN][1000 genomes]
rs6545381	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6545386	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6711105	0.89[ASN][1000 genomes]
rs6711217	0.86[ASN][1000 genomes]
rs6713088	0.90[JPT][hapmap]
rs6714450	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6715488	0.80[ASN][1000 genomes]
rs6721970	0.86[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes]
rs6743455	0.91[ASN][1000 genomes]
rs6746965	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs6748976	0.83[ASN][1000 genomes]
rs6748997	0.81[ASN][1000 genomes]
rs6751105	0.83[JPT][hapmap]
rs698855	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs72799298	0.83[ASN][1000 genomes]
rs72904908	0.81[ASN][1000 genomes]
rs7559384	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7565453	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7573551	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7576901	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7590819	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs805310	0.87[CHB][hapmap]
rs805321	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs805328	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs805351	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs805352	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs805365	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs805386	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs805399	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs805401	0.86[CHB][hapmap]
rs805404	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs805408	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs805426	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs9631059	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17045474	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54246800-54275200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:54248600-54278000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
4	chr2:54248800-54275600	Weak transcription	Primary B cells from cord blood	blood
5	chr2:54260400-54278200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:54266200-54281800	Weak transcription	Fetal Intestine Large	intestine
7	chr2:54268200-54275000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:54268200-54282400	Weak transcription	Right Ventricle	heart
9	chr2:54268400-54286800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:54268400-54290800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:54268600-54275400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr2:54268800-54275000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:54268800-54275400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:54268800-54278200	Weak transcription	Pancreas	Pancrea
15	chr2:54270200-54276600	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:54270400-54280200	Weak transcription	Ovary	ovary
17	chr2:54270800-54275400	Weak transcription	Primary T cells from cord blood	blood
18	chr2:54271200-54277000	Weak transcription	Aorta	Aorta
19	chr2:54271400-54286800	Weak transcription	HSMMtube	muscle
20	chr2:54271600-54278200	Weak transcription	Left Ventricle	heart
21	chr2:54271800-54278200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:54271800-54281600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:54272000-54280200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:54272000-54280600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:54272000-54286600	Weak transcription	HSMM	muscle
26	chr2:54272200-54275400	Weak transcription	NHEK	skin
27	chr2:54272200-54281600	Weak transcription	Brain Angular Gyrus	brain
28	chr2:54272200-54282800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:54272400-54276000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:54272400-54278200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:54272600-54275200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:54272600-54275400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr2:54272600-54278200	Weak transcription	Adipose Nuclei	Adipose
34	chr2:54272600-54278200	Weak transcription	Liver	Liver
35	chr2:54272600-54278200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:54272600-54278200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:54272600-54279800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:54272600-54280000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr2:54272600-54280000	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:54272600-54280000	Weak transcription	Brain Substantia Nigra	brain
41	chr2:54272600-54280000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:54272600-54280400	Weak transcription	Brain Germinal Matrix	brain
43	chr2:54272600-54286600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:54272600-54286800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:54272800-54278000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:54272800-54278000	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:54273000-54278400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:54273000-54292400	Weak transcription	Fetal Brain Female	brain
49	chr2:54273200-54275000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:54273200-54276600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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