Variant report

Variant	rs62140990
Chromosome Location	chr2:54280059-54280060
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54279730..54280237-chr2:54311516..54312403,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10496028	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11676462	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11683654	0.80[EUR][1000 genomes]
rs11890838	0.86[ASN][1000 genomes]
rs11893270	0.80[ASN][1000 genomes]
rs11896815	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11898855	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17039547	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17045474	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17045488	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2287643	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2357896	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34498089	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34773403	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671861	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55649409	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55705819	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56193146	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62137964	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62137976	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62137980	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62141002	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545381	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545386	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6714450	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6721970	0.84[AMR][1000 genomes]
rs7559384	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7565453	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7573551	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7576901	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590819	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv963233	chr2:54278282-54280313	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62140990	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
2	chr2:54266200-54281800	Weak transcription	Fetal Intestine Large	intestine
3	chr2:54268200-54282400	Weak transcription	Right Ventricle	heart
4	chr2:54268400-54286800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:54268400-54290800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:54270400-54280200	Weak transcription	Ovary	ovary
7	chr2:54271400-54286800	Weak transcription	HSMMtube	muscle
8	chr2:54271800-54281600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:54272000-54280200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:54272000-54280600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:54272000-54286600	Weak transcription	HSMM	muscle
12	chr2:54272200-54281600	Weak transcription	Brain Angular Gyrus	brain
13	chr2:54272200-54282800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:54272600-54280400	Weak transcription	Brain Germinal Matrix	brain
15	chr2:54272600-54286600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:54272600-54286800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:54273000-54292400	Weak transcription	Fetal Brain Female	brain
18	chr2:54274800-54280600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:54275800-54280200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:54276000-54280200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:54276200-54280200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr2:54276200-54280200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:54276200-54280200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:54276200-54280200	Weak transcription	HMEC	breast
25	chr2:54276200-54280400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:54276200-54280400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:54276200-54280400	Weak transcription	K562	blood
28	chr2:54276200-54281600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr2:54276200-54281600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:54276600-54280200	Weak transcription	Lung	lung
31	chr2:54276800-54280600	Weak transcription	Esophagus	oesophagus
32	chr2:54276800-54281000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:54276800-54286800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:54277000-54280400	Weak transcription	Placenta	Placenta
35	chr2:54277200-54280200	Weak transcription	Fetal Thymus	thymus
36	chr2:54277200-54281400	Weak transcription	HepG2	liver
37	chr2:54277200-54281800	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:54277200-54290800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:54277400-54280400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:54277600-54280200	Weak transcription	Aorta	Aorta
41	chr2:54278000-54280200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:54278000-54280400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:54278000-54280600	Strong transcription	Fetal Muscle Leg	muscle
44	chr2:54278200-54280200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr2:54278200-54280400	Strong transcription	Adipose Nuclei	Adipose
46	chr2:54278200-54280400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:54278200-54280600	Strong transcription	Primary B cells from cord blood	blood
48	chr2:54278200-54280600	Strong transcription	Liver	Liver
49	chr2:54278400-54280200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:54278400-54280600	Strong transcription	Primary T cells from cord blood	blood

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