Variant report

Variant	rs11694711
Chromosome Location	chr2:54199061-54199062
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:54195426-54199062	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr2:54198869-54199161	ProgFib	skin:	n/a	n/a
3	GATA1	chr2:54198061-54199105	PBDE	blood:	n/a	n/a
4	HEY1	chr2:54197829-54199069	HepG2	liver:	n/a	n/a
5	MTA3	chr2:54198225-54199158	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:54197173-54199820	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:54197077-54199214	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr2:54195490-54199155	PBDE	blood:	n/a	n/a
9	POLR2A	chr2:54197052-54199126	PFSK-1	brain:	n/a	n/a
10	TEAD4	chr2:54198069-54199174	HepG2	liver:	n/a	n/a
11	MXI1	chr2:54196016-54199237	IMR90	lung:	n/a	n/a
12	POLR2A	chr2:54196915-54199067	GM12891	blood:	n/a	n/a
13	POLR2A	chr2:54197545-54199110	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:54196330-54199220	IMR90	lung:	n/a	n/a
15	CHD1	chr2:54195365-54199244	IMR90	lung:	n/a	n/a
16	HEY1	chr2:54198773-54199206	HepG2	liver:	n/a	n/a
17	HCFC1	chr2:54197956-54199127	Hela-S3	cervix:	n/a	n/a
18	MXI1	chr2:54195676-54199239	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr2:54197010-54199267	H1-hESC	embryonic stem cell:	n/a	n/a
20	NR2F2	chr2:54198424-54199209	K562	blood:	n/a	n/a
21	POLR2A	chr2:54196472-54199174	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54198564..54201435-chr2:54359737..54361960,2	K562	blood:
2	chr2:54135813..54137897-chr2:54198410..54200281,2	K562	blood:
3	chr2:54157567..54166967-chr2:54194910..54201681,12	MCF-7	breast:
4	chr2:54197301..54199396-chr2:54783418..54785695,2	MCF-7	breast:
5	chr2:54176048..54178126-chr2:54198399..54200009,2	MCF-7	breast:
6	chr2:54014148..54016031-chr2:54196984..54199909,2	MCF-7	breast:
7	chr2:54174802..54180100-chr2:54196834..54199105,5	K562	blood:
8	chr2:54198790..54200475-chr2:54201295..54203717,2	K562	blood:

No data

Variant related genes	Relation type
PSME4	TF binding region
ENSG00000068878	Chromatin interaction
ENSG00000068912	Chromatin interaction
ENSG00000115306	Chromatin interaction
ENSG00000115239	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10084374	0.82[EUR][1000 genomes]
rs10167891	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10168293	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10181999	0.84[EUR][1000 genomes]
rs10183655	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10186566	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11674724	0.85[ASN][1000 genomes]
rs11683741	0.93[ASN][1000 genomes]
rs11689025	0.93[ASN][1000 genomes]
rs11893270	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13394278	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1477258	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17045452	0.94[ASN][1000 genomes]
rs2112122	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28653587	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28851028	0.81[ASN][1000 genomes]
rs2909459	0.96[ASN][1000 genomes]
rs2949815	0.95[ASN][1000 genomes]
rs3731967	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671742	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671746	0.84[ASN][1000 genomes]
rs4671747	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55692047	0.87[ASN][1000 genomes]
rs56302494	0.85[ASN][1000 genomes]
rs62139336	0.94[ASN][1000 genomes]
rs6545377	0.87[ASN][1000 genomes]
rs6545380	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66773232	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6711105	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6711217	0.81[EUR][1000 genomes]
rs6715488	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6742042	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6743455	0.84[EUR][1000 genomes]
rs6746965	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6748976	0.86[ASN][1000 genomes]
rs6748997	0.84[ASN][1000 genomes]
rs72799298	0.86[ASN][1000 genomes]
rs72904908	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7559947	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7564912	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7591431	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs805310	0.96[ASN][1000 genomes]
rs805344	0.96[ASN][1000 genomes]
rs805416	0.88[AMR][1000 genomes]
rs805448	0.83[AMR][1000 genomes]
rs9631059	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	esv3425017	chr2:54196873-54199421	Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11694711	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54194800-54199400	Active TSS	HSMMtube	muscle
2	chr2:54195000-54199200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:54195000-54199400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:54195200-54199200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr2:54195200-54199400	Active TSS	HSMM	muscle
6	chr2:54195400-54199200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:54195400-54199200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr2:54195400-54199200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr2:54195400-54199200	Active TSS	Psoas Muscle	Psoas
10	chr2:54195400-54199400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:54195600-54199200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr2:54195600-54199200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:54195800-54199200	Active TSS	H1 Cell Line	embryonic stem cell
14	chr2:54195800-54199200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:54195800-54199200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:54195800-54199200	Active TSS	Ovary	ovary
17	chr2:54195800-54199200	Active TSS	NHDF-Ad	bronchial
18	chr2:54196000-54199200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:54196000-54199200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:54196000-54199200	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr2:54196000-54199200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:54196000-54199200	Active TSS	NHLF	lung
23	chr2:54196000-54199400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:54196200-54199200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:54196200-54199200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:54196200-54199200	Active TSS	Brain Cingulate Gyrus	brain
27	chr2:54196200-54199200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:54196200-54199200	Active TSS	Colon Smooth Muscle	Colon
29	chr2:54196200-54199200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr2:54196400-54199200	Active TSS	Fetal Intestine Small	intestine
31	chr2:54196400-54199200	Active TSS	Fetal Kidney	kidney
32	chr2:54196400-54199200	Active TSS	Fetal Muscle Trunk	muscle
33	chr2:54196400-54199200	Active TSS	Fetal Stomach	stomach
34	chr2:54196400-54199200	Active TSS	A549	lung
35	chr2:54196600-54199200	Active TSS	Colonic Mucosa	Colon
36	chr2:54196800-54199200	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr2:54196800-54199200	Active TSS	Rectal Smooth Muscle	rectum
38	chr2:54197000-54199200	Active TSS	Pancreas	Pancrea
39	chr2:54197000-54199200	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr2:54197200-54199200	Active TSS	Fetal Brain Female	brain
41	chr2:54197800-54199200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:54197800-54199200	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr2:54198400-54199200	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr2:54198400-54199200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:54198600-54199200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:54198600-54199200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr2:54198600-54199200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr2:54198600-54199200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:54198600-54199200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr2:54198600-54199200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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