Variant report

Variant	rs10017460
Chromosome Location	chr4:57252941-57252942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr4:57252864-57254072	ECC-1	luminal epithelium:	n/a	n/a
2	FOXM1	chr4:57252937-57253969	ECC-1	luminal epithelium:	n/a	n/a
3	PML	chr4:57252923-57254296	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:57252843-57257309	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZNF384	chr4:57252891-57254041	GM12878	blood:	n/a	n/a
6	REST	chr4:57252837-57254482	H1-neurons	neurons:	n/a	chr4:57253697-57253710 chr4:57253417-57253431 chr4:57253709-57253719
7	POLR2A	chr4:57252887-57254837	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr4:57252908-57254160	HepG2	liver:	n/a	chr4:57253991-57254002
9	TAF1	chr4:57252896-57254031	H1-hESC	embryonic stem cell:	n/a	n/a
10	CEBPB	chr4:57252931-57253494	A549	lung:	n/a	n/a
11	CHD1	chr4:57252924-57253637	H1-hESC	embryonic stem cell:	n/a	n/a
12	ZNF384	chr4:57252854-57254266	K562	blood:	n/a	n/a
13	CEBPB	chr4:57252244-57254192	K562	blood:	n/a	chr4:57252450-57252463 chr4:57252452-57252461 chr4:57253991-57254002
14	MXI1	chr4:57252900-57254796	SK-N-SH	brain:	n/a	n/a
15	CEBPB	chr4:57252863-57254201	Hela-S3	cervix:	n/a	chr4:57253991-57254002
16	MYBL2	chr4:57252926-57254016	HepG2	liver:	n/a	n/a
17	CEBPB	chr4:57252898-57253508	K562	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57245776..57248590-chr4:57250681..57253317,2	MCF-7	breast:
2	chr4:57252171..57255208-chr4:57332200..57335252,5	K562	blood:
3	chr4:57252130..57255932-chr4:57332416..57336369,6	K562	blood:
4	chr4:57251780..57255283-chr4:57300557..57304376,5	MCF-7	breast:
5	chr4:57250870..57256510-chr4:57298204..57303491,14	K562	blood:
6	chr4:57252113..57256281-chr4:57265528..57268374,5	MCF-7	breast:
7	chr4:57251940..57255035-chr4:57332077..57334754,4	MCF-7	breast:
8	chr4:57249593..57251737-chr4:57251842..57253742,2	K562	blood:
9	chr4:57252573..57255971-chr4:57298663..57303783,6	MCF-7	breast:
10	chr4:57251883..57253946-chr4:57396755..57399062,3	K562	blood:
11	chr4:56813904..56818311-chr4:57252529..57254894,5	K562	blood:
12	chr4:57251518..57253690-chr4:57313439..57315337,2	K562	blood:
13	chr4:57252051..57253870-chr9:33289300..33291783,2	K562	blood:
14	chr4:57252189..57254981-chr4:57775973..57777493,2	MCF-7	breast:
15	chr4:57250870..57256080-chr4:57298204..57304153,16	K562	blood:
16	chr4:57252303..57254207-chr4:57266105..57268233,2	MCF-7	breast:

No data

Variant related genes	Relation type
AASDH	TF binding region
ENSG00000269921	TF binding region
ENSG00000086102	Chromatin interaction
ENSG00000249693	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000084093	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000174799	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10008223	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10013402	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10434444	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10434445	0.93[ASN][1000 genomes]
rs10461357	0.83[ASN][1000 genomes]
rs1060472	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11133442	0.86[ASN][1000 genomes]
rs1124569	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12498340	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12501334	0.94[ASN][1000 genomes]
rs12503412	0.94[ASN][1000 genomes]
rs12508008	0.81[ASN][1000 genomes]
rs12509542	0.81[ASN][1000 genomes]
rs12510712	0.82[ASN][1000 genomes]
rs12511770	0.84[ASN][1000 genomes]
rs12513091	0.81[ASN][1000 genomes]
rs12646890	0.81[ASN][1000 genomes]
rs1474179	0.89[ASN][1000 genomes]
rs17086696	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17086794	0.86[ASN][1000 genomes]
rs17086853	0.81[ASN][1000 genomes]
rs1967559	0.86[ASN][1000 genomes]
rs1983378	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2030366	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28510634	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28866881	0.94[ASN][1000 genomes]
rs4263445	0.86[ASN][1000 genomes]
rs4340842	0.85[ASN][1000 genomes]
rs4346704	0.84[ASN][1000 genomes]
rs4618376	0.81[ASN][1000 genomes]
rs4864579	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864580	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864583	0.94[ASN][1000 genomes]
rs4865088	0.86[ASN][1000 genomes]
rs4865089	0.87[ASN][1000 genomes]
rs4865092	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865103	0.83[ASN][1000 genomes]
rs4865107	0.81[ASN][1000 genomes]
rs5010012	0.95[ASN][1000 genomes]
rs56099714	0.81[ASN][1000 genomes]
rs56392224	0.94[ASN][1000 genomes]
rs56887793	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58151706	0.93[ASN][1000 genomes]
rs61032900	0.86[ASN][1000 genomes]
rs66858948	0.86[ASN][1000 genomes]
rs66863699	0.81[ASN][1000 genomes]
rs67957495	0.86[ASN][1000 genomes]
rs6820279	0.90[ASN][1000 genomes]
rs6820314	0.94[ASN][1000 genomes]
rs6821301	0.87[ASN][1000 genomes]
rs6829250	0.94[ASN][1000 genomes]
rs6832797	0.92[ASN][1000 genomes]
rs6834696	0.96[ASN][1000 genomes]
rs6849183	0.87[ASN][1000 genomes]
rs7664841	0.87[ASN][1000 genomes]
rs7670991	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8340	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10017460	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57207800-57253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr4:57216000-57253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:57223000-57253200	Weak transcription	Esophagus	oesophagus
4	chr4:57223200-57253200	Weak transcription	Gastric	stomach
5	chr4:57229800-57253000	Weak transcription	Ovary	ovary
6	chr4:57229800-57253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:57229800-57253200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:57232800-57253000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:57236600-57253000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:57236600-57253200	Weak transcription	Lung	lung
11	chr4:57236800-57253000	Weak transcription	Aorta	Aorta
12	chr4:57236800-57253000	Weak transcription	Left Ventricle	heart
13	chr4:57251800-57253000	Enhancers	Primary hematopoietic stem cells	blood
14	chr4:57251800-57253000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:57251800-57253000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:57251800-57254400	Active TSS	Hela-S3	cervix
17	chr4:57252000-57253000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:57252000-57253200	Weak transcription	Spleen	Spleen
19	chr4:57252200-57254400	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr4:57252200-57254600	Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr4:57252200-57255000	Active TSS	NHLF	lung
22	chr4:57252200-57255200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr4:57252200-57255200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:57252200-57255200	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr4:57252400-57253000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:57252400-57254000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:57252400-57254200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:57252400-57254400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:57252400-57254400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:57252400-57254400	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr4:57252400-57254400	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr4:57252400-57254400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:57252400-57254400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:57252400-57254400	Active TSS	Fetal Intestine Small	intestine
35	chr4:57252400-57254400	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr4:57252400-57254400	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr4:57252400-57254400	Active TSS	Stomach Smooth Muscle	stomach
38	chr4:57252400-57254400	Active TSS	HSMM	muscle
39	chr4:57252400-57254400	Active TSS	NH-A	brain
40	chr4:57252400-57254600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:57252400-57255000	Active TSS	H1 Cell Line	embryonic stem cell
42	chr4:57252400-57255000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:57252400-57255000	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr4:57252400-57255000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:57252400-57255200	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr4:57252400-57255400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:57252400-57255600	Active TSS	K562	blood
48	chr4:57252600-57253000	Weak transcription	Stomach Mucosa	stomach
49	chr4:57252600-57253200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:57252600-57253200	Active TSS	Duodenum Smooth Muscle	Duodenum

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