Variant report

Variant	rs56874024
Chromosome Location	chr3:134076316-134076317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:57)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:57 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:134075099-134077753	Hela-S3	cervix:	n/a	n/a
2	TEAD4	chr3:134075856-134077787	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr3:134075964-134077712	MCF-7	breast:	n/a	n/a
4	NR2F2	chr3:134076257-134077586	MCF-7	breast:	n/a	n/a
5	POLR2A	chr3:134076061-134077392	HepG2	liver:	n/a	n/a
6	GATA3	chr3:134076151-134077491	SK-N-SH	brain:	n/a	n/a
7	EP300	chr3:134075913-134077492	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:134075139-134077732	ECC-1	luminal epithelium:	n/a	n/a
9	TEAD4	chr3:134076242-134077194	MCF-7	breast:	n/a	n/a
10	POLR2A	chr3:134075304-134077814	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr3:134076090-134076591	A549	lung:	n/a	n/a
12	POLR2A	chr3:134076100-134077122	ProgFib	skin:	n/a	n/a
13	POLR2A	chr3:134075038-134079875	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr3:134075907-134077716	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:134074939-134079826	PANC-1	pancreas:	n/a	n/a
16	SIN3AK20	chr3:134076292-134077357	MCF-7	breast:	n/a	n/a
17	PBX3	chr3:134075932-134077653	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr3:134075808-134077598	U87	brain:	n/a	n/a
19	GTF2F1	chr3:134076203-134077303	Hela-S3	cervix:	n/a	n/a
20	CHD1	chr3:134070900-134094634	IMR90	lung:	n/a	chr3:134093783-134093793 chr3:134092557-134092567 chr3:134083055-134083065
21	TCF12	chr3:134076241-134077443	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr3:134075092-134079606	A549	lung:	n/a	n/a
23	MAZ	chr3:134075111-134077713	IMR90	lung:	n/a	n/a
24	YY1	chr3:134076259-134077250	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr3:134075129-134076368	HUVEC	blood vessel:	n/a	n/a
26	TEAD4	chr3:134076106-134077377	SK-N-SH	brain:	n/a	n/a
27	GATA3	chr3:134076073-134077287	MCF-7	breast:	n/a	n/a
28	MAX	chr3:134076273-134077872	ECC-1	luminal epithelium:	n/a	n/a
29	USF2	chr3:134075061-134077221	Hela-S3	cervix:	n/a	n/a
30	SIN3AK20	chr3:134075943-134077495	MCF-7	breast:	n/a	n/a
31	POLR2A	chr3:134075008-134079572	HUVEC	blood vessel:	n/a	n/a
32	HDAC2	chr3:134076240-134077165	MCF-7	breast:	n/a	n/a
33	POLR2A	chr3:134071087-134094366	Hela-S3	cervix:	n/a	n/a
34	JUND	chr3:134076251-134077400	SK-N-SH	brain:	n/a	chr3:134077134-134077146
35	POLR2A	chr3:134076196-134077306	MCF-7	breast:	n/a	n/a
36	POLR2A	chr3:134071303-134093679	HepG2	liver:	n/a	n/a
37	MAX	chr3:134076312-134077666	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr3:134075683-134078854	U87	brain:	n/a	n/a
39	EP300	chr3:134075816-134077866	ECC-1	luminal epithelium:	n/a	n/a
40	PBX3	chr3:134076008-134077386	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr3:134074967-134094367	PANC-1	pancreas:	n/a	n/a
42	HDAC2	chr3:134076298-134077289	MCF-7	breast:	n/a	n/a
43	POLR2A	chr3:134075815-134077429	SK-N-MC	brain:	n/a	n/a
44	TCF12	chr3:134076203-134077551	SK-N-SH	brain:	n/a	n/a
45	TCF12	chr3:134076301-134077645	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr3:134074945-134079788	H1-hESC	embryonic stem cell:	n/a	n/a
47	EP300	chr3:134076300-134077683	A549	lung:	n/a	n/a
48	GATA3	chr3:134076220-134077234	T-47D	breast:	n/a	n/a
49	MAX	chr3:134076267-134077201	MCF-7	breast:	n/a	n/a
50	POLR2A	chr3:134076153-134076365	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:134076315-134076365	SAEC	small airway:	n/a
2	chr3:134076315-134076365	U87	brain:	n/a
3	chr3:134076315-134076365	NH-A	brain:	n/a
4	chr3:134076315-134076365	HL-60	blood:	n/a
5	chr3:134076315-134076365	MCF-7	breast:	n/a
6	chr3:134076315-134076365	HCT-116	colon:	n/a
7	chr3:134076315-134076365	PANC-1	pancreas:	n/a
8	chr3:134076315-134076365	IMR90	lung:	fetal
9	chr3:134076315-134076365	MCF10A-Er-Src	breast:	n/a
10	chr3:134076315-134076365	AG04450	lung:	fetal
11	chr3:134076315-134076365	HNPCEpiC	eye:	n/a
12	chr3:134076315-134076365	BE2_C	brain:	n/a
13	chr3:134076315-134076365	HCM	heart:	n/a
14	chr3:134076315-134076365	GM06990	blood:	n/a
15	chr3:134076315-134076365	Caco-2	colon:	n/a
16	chr3:134076315-134076365	GM12891	blood:	n/a
17	chr3:134076315-134076365	HAEpiC	amniotic membrane:	n/a
18	chr3:134076315-134076365	Jurkat	blood:	n/a
19	chr3:134076315-134076365	GM12892	blood:	n/a
20	chr3:134076315-134076365	NHDF-neo	bronchial:	n/a
21	chr3:134076315-134076365	ProgFib	skin:	n/a
22	chr3:134076315-134076365	PrEC	prostate:	n/a
23	chr3:134076315-134076365	ECC-1	luminal epithelium:	n/a
24	chr3:134076315-134076365	AG04449	skin:	fetal
25	chr3:134076315-134076365	T-47D	breast:	n/a
26	chr3:134076315-134076365	A549	lung:	n/a
27	chr3:134076315-134076365	SKMC	muscle:	n/a
28	chr3:134076315-134076365	NHBE	bronchial:	n/a
29	chr3:134076315-134076365	PFSK-1	brain:	n/a
30	chr3:134076315-134076365	AG09319	gingival:	n/a
31	chr3:134076315-134076365	HRPEpiC	eye:	n/a
32	chr3:134076315-134076365	AG10803	skin:	n/a
33	chr3:134076315-134076365	ovcar-3	ovarian:	n/a
34	chr3:134076315-134076365	H1-hESC	embryonic stem cell:	embryo
35	chr3:134076315-134076365	HCF	heart:	n/a
36	chr3:134076315-134076365	GM12878	blood:	n/a
37	chr3:134076315-134076365	HMEC	breast:	n/a
38	chr3:134076315-134076365	NB4	blood:	n/a
39	chr3:134076315-134076365	Hepatocyte	liver:	n/a
40	chr3:134076315-134076365	RPTEC	kidney:	n/a
41	chr3:134076315-134076365	HIPEpiC	eye:	n/a
42	chr3:134076315-134076365	SK-N-MC	brain:	n/a
43	chr3:134076315-134076365	HRCEpiC	kidney:	n/a
44	chr3:134076315-134076365	HUVEC	blood vessel:	n/a
45	chr3:134076315-134076365	AoSMC	blood vessel:	n/a
46	chr3:134076315-134076365	BJ	skin:	n/a
47	chr3:134076315-134076365	HEK293	kidney:	embryo
48	chr3:134076315-134076365	AG09309	skin:	n/a
49	chr3:134076315-134076365	K562	blood:	n/a
50	chr3:134076315-134076365	SK-N-SH_RA	brain:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:134074631..134077411-chr3:134204905..134207486,2	MCF-7	breast:
2	chr3:134072948..134076764-chr3:134201781..134206077,4	MCF-7	breast:
3	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
4	chr3:134069007..134072370-chr3:134075638..134078854,3	K562	blood:
5	chr3:133966207..133969204-chr3:134075829..134077344,2	MCF-7	breast:

No data

Variant related genes	Relation type
RPL39P5	TF binding region
RPL39P5	CpG island
ENSG00000214289	Chromatin interaction
ENSG00000182923	Chromatin interaction
ENSG00000240006	Chromatin interaction
ENSG00000129055	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11925583	1.00[EUR][1000 genomes]
rs2173448	1.00[EUR][1000 genomes]
rs2400272	1.00[EUR][1000 genomes]
rs35161002	1.00[EUR][1000 genomes]
rs59473547	1.00[EUR][1000 genomes]
rs60048996	1.00[EUR][1000 genomes]
rs6798709	1.00[EUR][1000 genomes]
rs7433301	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7623024	1.00[EUR][1000 genomes]
rs7629849	1.00[EUR][1000 genomes]
rs7643419	1.00[EUR][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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134069200-134090000	Genic enhancers	Fetal Muscle Trunk	muscle
2	chr3:134069400-134089800	Genic enhancers	Fetal Muscle Leg	muscle
3	chr3:134070000-134082400	Genic enhancers	Right Ventricle	heart
4	chr3:134070400-134088200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:134071000-134082600	Genic enhancers	NHLF	lung
6	chr3:134071000-134088800	Enhancers	Right Atrium	heart
7	chr3:134071200-134082400	Genic enhancers	Brain Substantia Nigra	brain
8	chr3:134071400-134079000	Genic enhancers	Fetal Intestine Large	intestine
9	chr3:134071600-134076400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:134071600-134082200	Weak transcription	Primary T cells from cord blood	blood
11	chr3:134071600-134082800	Genic enhancers	Placenta	Placenta
12	chr3:134072000-134079000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:134072000-134082800	Genic enhancers	Lung	lung
14	chr3:134072200-134076600	Weak transcription	Fetal Thymus	thymus
15	chr3:134072200-134082400	Genic enhancers	Brain Hippocampus Middle	brain
16	chr3:134072200-134090200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:134072400-134076600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:134072400-134077200	Genic enhancers	Osteobl	bone
19	chr3:134072400-134091200	Genic enhancers	Spleen	Spleen
20	chr3:134072600-134080200	Weak transcription	Small Intestine	intestine
21	chr3:134072600-134082000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:134072600-134082200	Genic enhancers	Adipose Nuclei	Adipose
23	chr3:134072800-134077000	Genic enhancers	NHEK	skin
24	chr3:134072800-134081000	Genic enhancers	Placenta Amnion	Placenta Amnion
25	chr3:134072800-134082400	Genic enhancers	Brain Cingulate Gyrus	brain
26	chr3:134072800-134082600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:134072800-134090600	Genic enhancers	Left Ventricle	heart
28	chr3:134073000-134076600	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr3:134073000-134077600	Transcr. at gene 5' and 3'	A549	lung
30	chr3:134073000-134078400	Genic enhancers	Fetal Kidney	kidney
31	chr3:134073000-134080400	Genic enhancers	Ovary	ovary
32	chr3:134073000-134082200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:134073000-134089400	Genic enhancers	HMEC	breast
34	chr3:134073200-134076400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:134073200-134076600	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:134073200-134077200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
37	chr3:134073200-134078200	Genic enhancers	Fetal Lung	lung
38	chr3:134073200-134079400	Genic enhancers	Esophagus	oesophagus
39	chr3:134073200-134082000	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr3:134073200-134082200	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:134073400-134082200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
42	chr3:134073400-134091400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:134073800-134082400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:134074000-134077200	Genic enhancers	NH-A	brain
45	chr3:134074000-134077600	Enhancers	Fetal Heart	heart
46	chr3:134074400-134077200	Weak transcription	Fetal Brain Male	brain
47	chr3:134074400-134077200	Strong transcription	Fetal Brain Female	brain
48	chr3:134074400-134078800	Strong transcription	Liver	Liver
49	chr3:134074400-134082600	Genic enhancers	Brain Anterior Caudate	brain
50	chr3:134074400-134089400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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