Variant report

Variant	rs3116591
Chromosome Location	chr13:50570774-50570775
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:297)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:297 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:50570610-50570990	SK-N-MC	brain:	n/a	n/a
2	TBL1XR1	chr13:50570619-50570928	K562	blood:	n/a	n/a
3	POLR2A	chr13:50569618-50571827	GM19193	blood:	n/a	n/a
4	CHD2	chr13:50570279-50571333	K562	blood:	n/a	chr13:50570858-50570868
5	TCF12	chr13:50570567-50571908	ECC-1	luminal epithelium:	n/a	n/a
6	TAF1	chr13:50570718-50570978	GM12892	blood:	n/a	n/a
7	POLR2A	chr13:50570619-50571043	HUVEC	blood vessel:	n/a	n/a
8	HCFC1	chr13:50570363-50571837	K562	blood:	n/a	n/a
9	TBL1XR1	chr13:50569699-50571799	GM12878	blood:	n/a	n/a
10	CTBP2	chr13:50570547-50571643	H1-hESC	embryonic stem cell:	n/a	n/a
11	TAF1	chr13:50570583-50571024	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr13:50570603-50571046	K562	blood:	n/a	n/a
13	RELA	chr13:50569611-50571801	GM12891	blood:	n/a	n/a
14	TAF1	chr13:50570629-50571027	H1-neurons	neurons:	n/a	n/a
15	POU2F2	chr13:50570665-50571049	GM12878	blood:	n/a	n/a
16	ZC3H11A	chr13:50570737-50570828	K562	blood:	n/a	n/a
17	E2F6	chr13:50570703-50571025	K562	blood:	n/a	n/a
18	REST	chr13:50570246-50572731	H1-neurons	neurons:	n/a	chr13:50570689-50570702
19	ETS1	chr13:50570696-50571079	A549	lung:	n/a	chr13:50570737-50570748
20	ELK1	chr13:50570748-50570948	K562	blood:	n/a	n/a
21	BHLHE40	chr13:50570750-50571823	GM12878	blood:	n/a	n/a
22	POLR2A	chr13:50569733-50571768	Raji	blood:	n/a	n/a
23	POLR2A	chr13:50570381-50571754	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr13:50569475-50571004	GM12892	blood:	n/a	n/a
25	E2F6	chr13:50570715-50570994	K562	blood:	n/a	n/a
26	E2F6	chr13:50570716-50571023	H1-hESC	embryonic stem cell:	n/a	n/a
27	ZKSCAN1	chr13:50570710-50570946	Hela-S3	cervix:	n/a	n/a
28	ZNF384	chr13:50570547-50570797	GM12878	blood:	n/a	n/a
29	MXI1	chr13:50569870-50572252	SK-N-SH	brain:	n/a	n/a
30	MXI1	chr13:50570750-50570939	Hela-S3	cervix:	n/a	n/a
31	PBX3	chr13:50570641-50571020	A549	lung:	n/a	n/a
32	TEAD4	chr13:50570728-50571003	H1-hESC	embryonic stem cell:	n/a	n/a
33	HDAC2	chr13:50570495-50570954	H1-hESC	embryonic stem cell:	n/a	chr13:50570605-50570619
34	FOXP2	chr13:50570710-50571029	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr13:50569900-50571749	GM15510	blood:	n/a	n/a
36	PAX5	chr13:50570623-50571023	GM12878	blood:	n/a	n/a
37	PBX3	chr13:50570763-50571025	A549	lung:	n/a	n/a
38	POLR2A	chr13:50569712-50570994	GM12891	blood:	n/a	n/a
39	REST	chr13:50570697-50570987	PANC-1	pancreas:	n/a	n/a
40	HA-E2F1	chr13:50570189-50571931	MCF-7	breast:	n/a	chr13:50571525-50571535 chr13:50571593-50571602
41	POLR2A	chr13:50570535-50571008	ECC-1	luminal epithelium:	n/a	n/a
42	TCF12	chr13:50570533-50571008	A549	lung:	n/a	n/a
43	POLR2A	chr13:50569715-50571809	NB4	blood:	n/a	n/a
44	POLR2A	chr13:50570255-50571000	GM12878	blood:	n/a	n/a
45	TBP	chr13:50570622-50571850	K562	blood:	n/a	n/a
46	TAF1	chr13:50570665-50570993	SK-N-SH	brain:	n/a	n/a
47	HEY1	chr13:50570618-50570991	HepG2	liver:	n/a	chr13:50570747-50570762 chr13:50570689-50570704
48	ZEB1	chr13:50570630-50570884	GM12878	blood:	n/a	n/a
49	TAF1	chr13:50570595-50571004	K562	blood:	n/a	n/a
50	NFIC	chr13:50569419-50571022	GM12878	blood:	n/a	chr13:50570591-50570619

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:50510078..50512694-chr13:50569483..50571768,3	MCF-7	breast:
2	chr12:21810600..21811356-chr13:50570159..50570946,2	NB4	blood:
3	chr13:50507293..50510312-chr13:50568081..50571220,3	MCF-7	breast:
4	chr13:50509071..50511034-chr13:50570092..50572951,3	K562	blood:
5	chr13:50570675..50571337-chr6:27860603..27861378,2	Hela-S3	cervix:
6	chr13:50570665..50571474-chr13:50655702..50656445,2	NB4	blood:
7	chr13:50568991..50573569-chr13:50697831..50701767,8	K562	blood:
8	chr13:50365087..50367801-chr13:50569333..50572997,5	MCF-7	breast:
9	chr13:50242666..50244239-chr13:50569416..50571466,2	MCF-7	breast:
10	chr13:50570651..50571645-chr2:27545421..27545958,2	Hela-S3	cervix:
11	chr13:50569368..50571479-chr13:50698927..50701104,2	MCF-7	breast:
12	chr13:50569748..50573186-chr13:50654848..50657793,4	MCF-7	breast:
13	chr13:50569852..50573038-chr13:50651628..50659276,11	K562	blood:
14	chr11:67980278..67981274-chr13:50570488..50571441,2	NB4	blood:
15	chr13:50568781..50571479-chr13:50962860..50965023,2	K562	blood:
16	chr13:50569462..50575212-chr13:50651363..50657415,15	K562	blood:
17	chr13:50569315..50571977-chr13:50588593..50590941,4	K562	blood:
18	chr13:50569500..50573569-chr13:50696112..50701767,10	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRYD7-1	chr13:50567929-50570895	NONHSAT033771

No data

Variant related genes	Relation type
MIR3613	TF binding region
TRIM13	TF binding region
ENSG00000123178	Chromatin interaction
ENSG00000110066	Chromatin interaction
ENSG00000115204	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000198553	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000231607	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000203547	Chromatin interaction
ENSG00000111716	Chromatin interaction
ENSG00000176124	Chromatin interaction
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11617754	0.85[ASN][1000 genomes]
rs2066571	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2472599	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2475837	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2490636	0.80[AFR][1000 genomes]
rs28798976	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs73489861	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73489862	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs790943	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7986337	0.83[ASN][1000 genomes]
rs9568357	0.85[ASN][1000 genomes]
rs9568366	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50569400-50570800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr13:50569600-50572200	Active TSS	Brain Hippocampus Middle	brain
3	chr13:50569800-50571800	Active TSS	Duodenum Mucosa	Duodenum
4	chr13:50569800-50571800	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr13:50569800-50571800	Active TSS	Rectal Smooth Muscle	rectum
6	chr13:50569800-50571800	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr13:50569800-50572000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr13:50569800-50572000	Active TSS	Brain Angular Gyrus	brain
9	chr13:50569800-50572000	Active TSS	Brain Anterior Caudate	brain
10	chr13:50569800-50572000	Active TSS	Brain Cingulate Gyrus	brain
11	chr13:50569800-50572000	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr13:50569800-50572000	Active TSS	Fetal Stomach	stomach
13	chr13:50569800-50572200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr13:50569800-50572200	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr13:50569800-50572200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr13:50569800-50572200	Active TSS	Colon Smooth Muscle	Colon
17	chr13:50569800-50572200	Active TSS	HSMMtube	muscle
18	chr13:50569800-50573600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr13:50570000-50571200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr13:50570000-50571800	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr13:50570000-50571800	Active TSS	Small Intestine	intestine
22	chr13:50570000-50572000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:50570000-50572000	Active TSS	Ovary	ovary
24	chr13:50570000-50572200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr13:50570000-50572200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr13:50570000-50572200	Active TSS	Fetal Brain Female	brain
27	chr13:50570000-50572200	Active TSS	Psoas Muscle	Psoas
28	chr13:50570000-50572200	Active TSS	Hela-S3	cervix
29	chr13:50570000-50572400	Active TSS	Fetal Muscle Trunk	muscle
30	chr13:50570000-50572600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr13:50570000-50572600	Active TSS	Colonic Mucosa	Colon
32	chr13:50570000-50572800	Active TSS	Aorta	Aorta
33	chr13:50570000-50572800	Active TSS	Right Atrium	heart
34	chr13:50570000-50574000	Active TSS	H9 Cell Line	embryonic stem cell
35	chr13:50570200-50570800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr13:50570200-50571200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr13:50570200-50571600	Active TSS	Liver	Liver
38	chr13:50570200-50571600	Active TSS	Spleen	Spleen
39	chr13:50570200-50571600	Active TSS	Monocytes-CD14+_RO01746	blood
40	chr13:50570200-50571800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr13:50570200-50571800	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr13:50570200-50571800	Active TSS	Fetal Lung	lung
43	chr13:50570200-50571800	Active TSS	Gastric	stomach
44	chr13:50570200-50571800	Active TSS	Pancreas	Pancrea
45	chr13:50570200-50572000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr13:50570200-50572000	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr13:50570200-50572000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr13:50570200-50572000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr13:50570200-50572000	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr13:50570200-50572000	Active TSS	Fetal Adrenal Gland	Adrenal Gland

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