Variant report

Variant	rs2949815
Chromosome Location	chr2:54198295-54198296
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:381)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:381 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr2:54197955-54198664	GM12892	blood:	n/a	chr2:54198627-54198649 chr2:54198627-54198637
2	CREB1	chr2:54197809-54198588	K562	blood:	n/a	n/a
3	TAF1	chr2:54197941-54198524	HepG2	liver:	n/a	n/a
4	STAT5A	chr2:54197979-54198733	GM12878	blood:	n/a	n/a
5	PML	chr2:54197954-54198472	GM12878	blood:	n/a	n/a
6	MAX	chr2:54197854-54198592	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr2:54197686-54198623	MCF-7	breast:	n/a	n/a
8	POLR2A	chr2:54195426-54199062	MCF10A-Er-Src	breast:	n/a	n/a
9	RFX5	chr2:54198035-54198357	Hela-S3	cervix:	n/a	n/a
10	CCNT2	chr2:54197273-54198550	K562	blood:	n/a	chr2:54197374-54197383
11	SP1	chr2:54197882-54198539	A549	lung:	n/a	n/a
12	FOXA1	chr2:54198056-54198879	HepG2	liver:	n/a	n/a
13	FOS	chr2:54198056-54198362	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr2:54197845-54198687	H1-neurons	neurons:	n/a	n/a
15	TAF1	chr2:54198026-54198458	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr2:54197906-54198697	K562	blood:	n/a	n/a
17	ZBTB7A	chr2:54197589-54198547	K562	blood:	n/a	n/a
18	MYC	chr2:54197951-54198842	A549	lung:	n/a	n/a
19	POLR2A	chr2:54196963-54198609	GM18505	blood:	n/a	n/a
20	REST	chr2:54198015-54198513	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr2:54197807-54198620	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr2:54197971-54198437	GM12891	blood:	n/a	n/a
23	CREB1	chr2:54197961-54198304	A549	lung:	n/a	n/a
24	CTCF	chr2:54198260-54198410	WERI-Rb-1	eye:	n/a	n/a
25	GATA1	chr2:54198061-54199105	PBDE	blood:	n/a	n/a
26	MAX	chr2:54197910-54198694	NB4	blood:	n/a	n/a
27	MYC	chr2:54197930-54198525	MCF-7	breast:	n/a	n/a
28	SIN3A	chr2:54196870-54198934	H1-hESC	embryonic stem cell:	n/a	chr2:54197564-54197573
29	POLR2A	chr2:54197936-54198575	GM12891	blood:	n/a	n/a
30	YY1	chr2:54197647-54198553	K562	blood:	n/a	n/a
31	JUND	chr2:54198056-54198627	H1-hESC	embryonic stem cell:	n/a	n/a
32	MYC	chr2:54197983-54198674	H1-hESC	embryonic stem cell:	n/a	n/a
33	E2F6	chr2:54198047-54198626	A549	lung:	n/a	n/a
34	JUND	chr2:54198229-54198559	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr2:54197529-54198535	K562	blood:	n/a	n/a
36	POLR2A	chr2:54197216-54198783	NB4	blood:	n/a	n/a
37	POLR2A	chr2:54197866-54198532	K562	blood:	n/a	n/a
38	EP300	chr2:54198246-54198473	GM12878	blood:	n/a	n/a
39	RAD21	chr2:54198164-54198343	K562	blood:	n/a	n/a
40	GABPA	chr2:54197914-54198571	SK-N-SH	brain:	n/a	n/a
41	E2F6	chr2:54197952-54198507	K562	blood:	n/a	n/a
42	HEY1	chr2:54197829-54199069	HepG2	liver:	n/a	n/a
43	POLR2A	chr2:54197116-54198687	HUVEC	blood vessel:	n/a	n/a
44	MAZ	chr2:54197384-54198464	Hela-S3	cervix:	n/a	n/a
45	HNF4A	chr2:54197951-54198485	HepG2	liver:	n/a	n/a
46	POLR2A	chr2:54197346-54198630	MCF-7	breast:	n/a	n/a
47	ETS1	chr2:54197977-54198503	GM12878	blood:	n/a	n/a
48	MXI1	chr2:54196383-54198843	HepG2	liver:	n/a	n/a
49	POLR2A	chr2:54197956-54198571	Hela-S3	cervix:	n/a	n/a
50	TCF12	chr2:54198179-54198372	GM12878	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54174064..54177025-chr2:54196606..54198334,2	K562	blood:
2	chr2:8821873..8822528-chr2:54198116..54198697,2	HCT-116	colon:
3	chr1:154377822..154378480-chr2:54197817..54198522,2	HCT-116	colon:
4	chr17:7387527..7388173-chr2:54197783..54198746,2	Hela-S3	cervix:
5	chr2:54157567..54166967-chr2:54194910..54201681,12	MCF-7	breast:
6	chr2:54197301..54199396-chr2:54783418..54785695,2	MCF-7	breast:
7	chr2:54014148..54016031-chr2:54196984..54199909,2	MCF-7	breast:
8	chr2:54196743..54198781-chr2:54341566..54344110,2	K562	blood:
9	chr2:54174802..54180100-chr2:54196834..54199105,5	K562	blood:
10	chr2:54197595..54198318-chr8:29207753..29208664,2	HCT-116	colon:
11	chr17:62222840..62223549-chr2:54197639..54198401,2	HCT-116	colon:
12	chr2:54197865..54198700-chr2:85581464..85582262,2	Hela-S3	cervix:
13	chr14:70078032..70078862-chr2:54197449..54198389,2	Hela-S3	cervix:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACYP2-1	chr2:54198245-54198458	ENSG00000239235.3
2	lnc-ACYP2-1	chr2:54197975-54198458	ENSG00000239235.3

No data

Variant related genes	Relation type
PSME4	TF binding region
ENSG00000199753	Chromatin interaction
ENSG00000160712	Chromatin interaction
ENSG00000266402	Chromatin interaction
ENSG00000068912	Chromatin interaction
ENSG00000042445	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000235092	Chromatin interaction
ENSG00000120875	Chromatin interaction
ENSG00000115239	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000115306	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000100647	Chromatin interaction
ENSG00000115738	Chromatin interaction
ENSG00000115459	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10167891	0.85[ASN][1000 genomes]
rs10168293	0.96[ASN][1000 genomes]
rs10183655	0.91[ASN][1000 genomes]
rs11674724	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11683741	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11689025	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11694711	0.95[ASN][1000 genomes]
rs11890838	0.80[EUR][1000 genomes]
rs13394278	0.86[ASN][1000 genomes]
rs1477258	0.83[ASN][1000 genomes]
rs17045452	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2302879	0.82[AMR][1000 genomes]
rs28653587	0.86[ASN][1000 genomes]
rs28851028	0.82[ASN][1000 genomes]
rs2909459	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3731967	0.92[ASN][1000 genomes]
rs4671742	0.93[ASN][1000 genomes]
rs4671746	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4671747	0.81[ASN][1000 genomes]
rs55692047	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56302494	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62139336	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6545377	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66773232	0.91[ASN][1000 genomes]
rs6715488	0.85[ASN][1000 genomes]
rs6746965	0.84[ASN][1000 genomes]
rs6748976	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6748997	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72799298	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72904908	0.85[ASN][1000 genomes]
rs7559947	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7564912	0.86[ASN][1000 genomes]
rs7591431	0.86[ASN][1000 genomes]
rs805310	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805312	0.82[AMR][1000 genomes]
rs805323	0.82[AMR][1000 genomes]
rs805328	0.82[AMR][1000 genomes]
rs805329	0.81[AMR][1000 genomes]
rs805334	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs805344	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805346	0.82[AMR][1000 genomes]
rs805347	0.82[AMR][1000 genomes]
rs805348	0.80[AMR][1000 genomes]
rs805349	0.81[AMR][1000 genomes]
rs805351	0.83[AMR][1000 genomes]
rs805352	0.83[AMR][1000 genomes]
rs805354	0.83[AMR][1000 genomes]
rs805355	0.83[AMR][1000 genomes]
rs805356	0.83[AMR][1000 genomes]
rs805357	0.83[AMR][1000 genomes]
rs805362	0.83[AMR][1000 genomes]
rs805365	0.81[AMR][1000 genomes]
rs805447	0.82[AFR][1000 genomes]
rs805452	0.82[AFR][1000 genomes]
rs9631059	0.83[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
rs2949815	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54194000-54198800	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr2:54194800-54198800	Active TSS	Osteobl	bone
3	chr2:54194800-54199400	Active TSS	HSMMtube	muscle
4	chr2:54195000-54198800	Active TSS	HMEC	breast
5	chr2:54195000-54199200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr2:54195000-54199400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:54195200-54199200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr2:54195200-54199400	Active TSS	HSMM	muscle
9	chr2:54195400-54198600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr2:54195400-54199000	Active TSS	Left Ventricle	heart
11	chr2:54195400-54199000	Active TSS	Right Ventricle	heart
12	chr2:54195400-54199200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:54195400-54199200	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr2:54195400-54199200	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr2:54195400-54199200	Active TSS	Psoas Muscle	Psoas
16	chr2:54195400-54199400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:54195600-54198800	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr2:54195600-54198800	Active TSS	Stomach Smooth Muscle	stomach
19	chr2:54195600-54199000	Active TSS	Aorta	Aorta
20	chr2:54195600-54199000	Active TSS	Fetal Muscle Leg	muscle
21	chr2:54195600-54199200	Active TSS	H9 Cell Line	embryonic stem cell
22	chr2:54195600-54199200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:54195800-54198800	Active TSS	K562	blood
24	chr2:54195800-54198800	Active TSS	NHEK	skin
25	chr2:54195800-54199000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:54195800-54199000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:54195800-54199200	Active TSS	H1 Cell Line	embryonic stem cell
28	chr2:54195800-54199200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:54195800-54199200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:54195800-54199200	Active TSS	Ovary	ovary
31	chr2:54195800-54199200	Active TSS	NHDF-Ad	bronchial
32	chr2:54196000-54198400	Active TSS	NH-A	brain
33	chr2:54196000-54198600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:54196000-54198600	Active TSS	Brain Angular Gyrus	brain
35	chr2:54196000-54198600	Active TSS	Hela-S3	cervix
36	chr2:54196000-54198800	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr2:54196000-54198800	Active TSS	Fetal Thymus	thymus
38	chr2:54196000-54199000	Active TSS	GM12878-XiMat	blood
39	chr2:54196000-54199200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:54196000-54199200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:54196000-54199200	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr2:54196000-54199200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:54196000-54199200	Active TSS	NHLF	lung
44	chr2:54196000-54199400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:54196200-54198400	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr2:54196200-54198400	Active TSS	HUVEC	blood vessel
47	chr2:54196200-54198600	Active TSS	Muscle Satellite Cultured Cells	--
48	chr2:54196200-54198800	Active TSS	Brain Anterior Caudate	brain
49	chr2:54196200-54199200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:54196200-54199200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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