Variant report

Variant	rs3821705
Chromosome Location	chr3:134077001-134077002
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:184)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:184 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr3:134076836-134077154	MCF10A-Er-Src	breast:	n/a	n/a
2	YY1	chr3:134076668-134077454	ECC-1	luminal epithelium:	n/a	n/a
3	STAT3	chr3:134076751-134077150	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr3:134076820-134077706	IMR90	lung:	n/a	n/a
5	CHD2	chr3:134076621-134077214	Hela-S3	cervix:	n/a	n/a
6	NFIC	chr3:134076423-134077891	ECC-1	luminal epithelium:	n/a	n/a
7	SMC3	chr3:134076418-134077746	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:134075099-134077753	Hela-S3	cervix:	n/a	n/a
9	RAD21	chr3:134076323-134077704	IMR90	lung:	n/a	n/a
10	USF1	chr3:134076811-134077023	A549	lung:	n/a	n/a
11	MXI1	chr3:134076568-134077214	Hela-S3	cervix:	n/a	n/a
12	TEAD4	chr3:134075856-134077787	ECC-1	luminal epithelium:	n/a	n/a
13	TEAD4	chr3:134076608-134077279	A549	lung:	n/a	n/a
14	POLR2A	chr3:134076638-134077196	SK-N-MC	brain:	n/a	n/a
15	MAX	chr3:134075964-134077712	MCF-7	breast:	n/a	n/a
16	NR2F2	chr3:134076257-134077586	MCF-7	breast:	n/a	n/a
17	EP300	chr3:134076485-134077691	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr3:134076061-134077392	HepG2	liver:	n/a	n/a
19	STAT3	chr3:134076763-134077173	MCF10A-Er-Src	breast:	n/a	n/a
20	FOS	chr3:134076741-134077144	MCF10A-Er-Src	breast:	n/a	n/a
21	RAD21	chr3:134076745-134077149	SK-N-SH_RA	brain:	n/a	n/a
22	FOSL2	chr3:134076513-134077197	A549	lung:	n/a	chr3:134077134-134077146
23	USF1	chr3:134076813-134077034	A549	lung:	n/a	n/a
24	GATA3	chr3:134076151-134077491	SK-N-SH	brain:	n/a	n/a
25	RAD21	chr3:134076524-134077704	Hela-S3	cervix:	n/a	n/a
26	EP300	chr3:134075913-134077492	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr3:134075139-134077732	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr3:134076696-134077005	HCT-116	colon:	n/a	n/a
29	TCF7L2	chr3:134076646-134077037	PANC-1	pancreas:	n/a	chr3:134076821-134076835
30	MAX	chr3:134076527-134077690	Hela-S3	cervix:	n/a	n/a
31	BCL3	chr3:134076587-134077150	A549	lung:	n/a	n/a
32	TEAD4	chr3:134076242-134077194	MCF-7	breast:	n/a	n/a
33	POLR2A	chr3:134075304-134077814	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr3:134076454-134078848	HUVEC	blood vessel:	n/a	n/a
35	ZBTB7A	chr3:134076639-134077609	ECC-1	luminal epithelium:	n/a	chr3:134077332-134077341
36	FOSL2	chr3:134076324-134077302	SK-N-SH	brain:	n/a	chr3:134077134-134077146
37	POLR2A	chr3:134076100-134077122	ProgFib	skin:	n/a	n/a
38	TEAD4	chr3:134076663-134077073	H1-hESC	embryonic stem cell:	n/a	n/a
39	EP300	chr3:134076783-134077031	HepG2	liver:	n/a	n/a
40	POLR2A	chr3:134076385-134077670	SK-N-SH	brain:	n/a	n/a
41	EP300	chr3:134076387-134077224	T-47D	breast:	n/a	n/a
42	NFIC	chr3:134076336-134077749	ECC-1	luminal epithelium:	n/a	n/a
43	USF1	chr3:134076738-134077083	A549	lung:	n/a	n/a
44	TEAD4	chr3:134076322-134077416	SK-N-SH	brain:	n/a	n/a
45	FOXA2	chr3:134076789-134077030	HepG2	liver:	n/a	n/a
46	E2F6	chr3:134076572-134077126	A549	lung:	n/a	n/a
47	TCF7L2	chr3:134076403-134077405	Hela-S3	cervix:	n/a	chr3:134076821-134076835
48	POLR2A	chr3:134075038-134079875	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr3:134075907-134077716	H1-hESC	embryonic stem cell:	n/a	n/a
50	RAD21	chr3:134076726-134077002	HepG2	liver:	n/a	n/a

No data

(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	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
3	chr3:134069007..134072370-chr3:134075638..134078854,3	K562	blood:
4	chr3:133966207..133969204-chr3:134075829..134077344,2	MCF-7	breast:
5	chr3:134076345..134078417-chr3:134195768..134197623,2	MCF-7	breast:

No data

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

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10755085	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10755086	0.84[ASN][1000 genomes]
rs1111516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11708815	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11719057	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12495847	0.80[ASN][1000 genomes]
rs12496438	0.84[ASN][1000 genomes]
rs13075185	0.95[ASN][1000 genomes]
rs13322269	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs1353776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1353777	0.80[ASN][1000 genomes]
rs1353778	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1466827	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1498731	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1603824	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1863910	0.80[ASN][1000 genomes]
rs2133307	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2303635	0.89[CHB][hapmap]
rs2400278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2400279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2400280	0.88[ASN][1000 genomes]
rs34341902	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35951257	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755762	0.84[ASN][1000 genomes]
rs3773820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4264700	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4974485	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974486	1.00[JPT][hapmap]
rs4974489	0.90[ASN][1000 genomes]
rs4974491	0.90[ASN][1000 genomes]
rs4974494	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974495	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974496	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4974497	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439478	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786148	0.90[ASN][1000 genomes]
rs7613066	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9450	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817900	0.90[ASN][1000 genomes]
rs9853621	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[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	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3821705	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs3821705	RP11-375I20.6	cis	Artery Tibial	GTEx
rs3821705	RP11-375I20.6	cis	Esophagus Muscularis	GTEx
rs3821705	RP11-375I20.6	cis	Artery Aorta	GTEx
rs3821705	RP11-375I20.6	cis	Heart Left Ventricle	GTEx
rs3821705	RP11-375I20.6	cis	lung	GTEx
rs3821705	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs3821705	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx
rs3821705	RP11-375I20.6	cis	Thyroid	GTEx

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	chr3:134071600-134082200	Weak transcription	Primary T cells from cord blood	blood
10	chr3:134071600-134082800	Genic enhancers	Placenta	Placenta
11	chr3:134072000-134079000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:134072000-134082800	Genic enhancers	Lung	lung
13	chr3:134072200-134082400	Genic enhancers	Brain Hippocampus Middle	brain
14	chr3:134072200-134090200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:134072400-134077200	Genic enhancers	Osteobl	bone
16	chr3:134072400-134091200	Genic enhancers	Spleen	Spleen
17	chr3:134072600-134080200	Weak transcription	Small Intestine	intestine
18	chr3:134072600-134082000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:134072600-134082200	Genic enhancers	Adipose Nuclei	Adipose
20	chr3:134072800-134081000	Genic enhancers	Placenta Amnion	Placenta Amnion
21	chr3:134072800-134082400	Genic enhancers	Brain Cingulate Gyrus	brain
22	chr3:134072800-134082600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:134072800-134090600	Genic enhancers	Left Ventricle	heart
24	chr3:134073000-134077600	Transcr. at gene 5' and 3'	A549	lung
25	chr3:134073000-134078400	Genic enhancers	Fetal Kidney	kidney
26	chr3:134073000-134080400	Genic enhancers	Ovary	ovary
27	chr3:134073000-134082200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:134073000-134089400	Genic enhancers	HMEC	breast
29	chr3:134073200-134077200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
30	chr3:134073200-134078200	Genic enhancers	Fetal Lung	lung
31	chr3:134073200-134079400	Genic enhancers	Esophagus	oesophagus
32	chr3:134073200-134082000	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr3:134073200-134082200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:134073400-134082200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:134073400-134091400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr3:134073800-134082400	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:134074000-134077200	Genic enhancers	NH-A	brain
38	chr3:134074000-134077600	Enhancers	Fetal Heart	heart
39	chr3:134074400-134077200	Weak transcription	Fetal Brain Male	brain
40	chr3:134074400-134077200	Strong transcription	Fetal Brain Female	brain
41	chr3:134074400-134078800	Strong transcription	Liver	Liver
42	chr3:134074400-134082600	Genic enhancers	Brain Anterior Caudate	brain
43	chr3:134074400-134089400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:134075000-134090400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:134075200-134077200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:134075200-134078000	Genic enhancers	Stomach Mucosa	stomach
47	chr3:134075200-134081000	Genic enhancers	Gastric	stomach
48	chr3:134075200-134082200	Genic enhancers	Brain Inferior Temporal Lobe	brain
49	chr3:134075200-134082400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:134075200-134082800	Genic enhancers	Brain Angular Gyrus	brain

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