Variant report

Variant	rs4671742
Chromosome Location	chr2:54211624-54211625
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54196698..54199249-chr2:54209378..54211786,2	MCF-7	breast:
2	chr2:54196641..54201530-chr2:54208327..54212751,6	K562	blood:
3	chr2:54209836..54212670-chr2:54227485..54229972,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068878	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10084374	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10167891	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10168293	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10181999	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10183655	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10186566	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11674724	0.87[ASN][1000 genomes]
rs11683741	0.95[ASN][1000 genomes]
rs11689025	0.95[ASN][1000 genomes]
rs11694711	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11893270	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13394278	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1477258	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17045452	0.96[ASN][1000 genomes]
rs2112122	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28653587	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28851028	0.83[ASN][1000 genomes]
rs2909459	0.94[ASN][1000 genomes]
rs2949815	0.93[ASN][1000 genomes]
rs3731967	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671746	0.86[ASN][1000 genomes]
rs4671747	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55692047	0.89[ASN][1000 genomes]
rs56302494	0.87[ASN][1000 genomes]
rs62139336	0.96[ASN][1000 genomes]
rs6545377	0.89[ASN][1000 genomes]
rs6545380	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545381	0.80[ASN][1000 genomes]
rs66773232	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6711105	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6711217	0.82[EUR][1000 genomes]
rs6714450	0.81[ASN][1000 genomes]
rs6715488	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742042	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6743455	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6746965	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6748976	0.88[ASN][1000 genomes]
rs6748997	0.86[ASN][1000 genomes]
rs72799298	0.88[ASN][1000 genomes]
rs72904908	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7559947	0.96[ASN][1000 genomes]
rs7564912	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7591431	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs805310	0.94[ASN][1000 genomes]
rs805344	0.94[ASN][1000 genomes]
rs805416	0.83[AMR][1000 genomes]
rs9631059	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4671742	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54198600-54212000	Weak transcription	Spleen	Spleen
2	chr2:54199000-54214200	Weak transcription	Stomach Mucosa	stomach
3	chr2:54199000-54214400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:54199000-54215600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:54199000-54221600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:54199000-54228800	Weak transcription	Aorta	Aorta
7	chr2:54199200-54213800	Weak transcription	Psoas Muscle	Psoas
8	chr2:54199200-54213800	Weak transcription	Small Intestine	intestine
9	chr2:54199200-54214200	Weak transcription	Colonic Mucosa	Colon
10	chr2:54199200-54214200	Weak transcription	Fetal Heart	heart
11	chr2:54199200-54214200	Weak transcription	Fetal Kidney	kidney
12	chr2:54199200-54214200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:54199200-54214200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:54199200-54214200	Weak transcription	NH-A	brain
15	chr2:54199200-54214400	Weak transcription	A549	lung
16	chr2:54199200-54214600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:54200000-54214200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:54200200-54212800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:54200200-54216600	Weak transcription	Right Ventricle	heart
20	chr2:54200400-54218400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:54202200-54212600	Weak transcription	HepG2	liver
22	chr2:54202600-54211800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:54202600-54214200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:54202600-54214400	Weak transcription	NHDF-Ad	bronchial
25	chr2:54202800-54214800	Weak transcription	NHLF	lung
26	chr2:54202800-54215800	Weak transcription	NHEK	skin
27	chr2:54203200-54214200	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:54203600-54214800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:54203800-54214200	Weak transcription	Brain Anterior Caudate	brain
30	chr2:54204400-54226400	Weak transcription	Pancreas	Pancrea
31	chr2:54204600-54214000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:54204600-54214200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:54205000-54213800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:54205200-54222600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:54205800-54212400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:54206000-54212800	Weak transcription	Left Ventricle	heart
37	chr2:54206000-54214200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr2:54206000-54214200	Weak transcription	GM12878-XiMat	blood
39	chr2:54206000-54216600	Weak transcription	Esophagus	oesophagus
40	chr2:54206000-54221600	Weak transcription	Thymus	Thymus
41	chr2:54206000-54226400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:54206200-54214200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:54206200-54214200	Weak transcription	Adipose Nuclei	Adipose
44	chr2:54206200-54214200	Weak transcription	Brain Hippocampus Middle	brain
45	chr2:54206200-54214200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:54206200-54214200	Weak transcription	Brain Substantia Nigra	brain
47	chr2:54206200-54214400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:54206400-54220000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr2:54207800-54213000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:54208200-54211800	Weak transcription	Monocytes-CD14+_RO01746	blood

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