Variant report

Variant	rs9450
Chromosome Location	chr3:134075326-134075327
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

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	POLR2A	chr3:134075139-134077732	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr3:134075304-134077814	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr3:134075137-134075539	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:134075038-134079875	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr3:134074939-134079826	PANC-1	pancreas:	n/a	n/a
7	CHD1	chr3:134070900-134094634	IMR90	lung:	n/a	chr3:134093783-134093793 chr3:134092557-134092567 chr3:134083055-134083065
8	POLR2A	chr3:134075092-134079606	A549	lung:	n/a	n/a
9	POLR2A	chr3:134075106-134076303	HUVEC	blood vessel:	n/a	n/a
10	MAZ	chr3:134075111-134077713	IMR90	lung:	n/a	n/a
11	POLR2A	chr3:134075129-134076368	HUVEC	blood vessel:	n/a	n/a
12	USF2	chr3:134075061-134077221	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr3:134075008-134079572	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:134071087-134094366	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr3:134071303-134093679	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:134075276-134075372	ProgFib	skin:	n/a	n/a
17	POLR2A	chr3:134074967-134094367	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr3:134075106-134075846	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr3:134074945-134079788	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr3:134075153-134075368	HepG2	liver:	n/a	n/a
21	POLR2A	chr3:134069355-134094620	IMR90	lung:	n/a	n/a
22	POLR2A	chr3:134075053-134079865	SK-N-SH	brain:	n/a	n/a

No data

(count:3 , 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:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CEP63-4	chr3:134075075-134075740	refGeneNc_1711_NR_002811
2	lnc-AMOTL2-3	chr3:134075217-134075403	NONHSAT092235

No data

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

Extended variants
information (count: 36 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1111516	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708815	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11719057	0.90[ASN][1000 genomes]
rs13075185	0.90[ASN][1000 genomes]
rs1353776	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1353778	0.81[AMR][1000 genomes]
rs1466827	0.86[ASN][1000 genomes]
rs1498731	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1603824	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133307	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400279	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400280	0.93[ASN][1000 genomes]
rs34341902	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35951257	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732852	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773820	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3821705	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4264700	0.95[ASN][1000 genomes]
rs4974485	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974487	0.84[ASN][1000 genomes]
rs4974489	0.95[ASN][1000 genomes]
rs4974491	0.95[ASN][1000 genomes]
rs4974494	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974495	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974496	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974497	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439477	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439478	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786148	0.95[ASN][1000 genomes]
rs7613066	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9817900	0.95[ASN][1000 genomes]
rs9853621	0.95[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
rs9450	RP11-375I20.6	cis	Artery Aorta	GTEx
rs9450	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs9450	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs9450	RP11-375I20.6	cis	Thyroid	GTEx
rs9450	RP11-375I20.6	cis	lung	GTEx
rs9450	RP11-375I20.6	cis	Artery Tibial	GTEx
rs9450	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx
rs9450	RP11-375I20.6	cis	Esophagus Muscularis	GTEx
rs9450	RP11-375I20.6	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134066600-134076200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:134067600-134076200	Strong transcription	Brain Germinal Matrix	brain
3	chr3:134068400-134076000	Strong transcription	Fetal Stomach	stomach
4	chr3:134069000-134076000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:134069200-134090000	Genic enhancers	Fetal Muscle Trunk	muscle
6	chr3:134069400-134089800	Genic enhancers	Fetal Muscle Leg	muscle
7	chr3:134070000-134082400	Genic enhancers	Right Ventricle	heart
8	chr3:134070400-134088200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:134071000-134075800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:134071000-134082600	Genic enhancers	NHLF	lung
11	chr3:134071000-134088800	Enhancers	Right Atrium	heart
12	chr3:134071200-134082400	Genic enhancers	Brain Substantia Nigra	brain
13	chr3:134071400-134079000	Genic enhancers	Fetal Intestine Large	intestine
14	chr3:134071600-134076000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:134071600-134076400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:134071600-134082200	Weak transcription	Primary T cells from cord blood	blood
17	chr3:134071600-134082800	Genic enhancers	Placenta	Placenta
18	chr3:134071800-134075400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:134072000-134079000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:134072000-134082800	Genic enhancers	Lung	lung
21	chr3:134072200-134076600	Weak transcription	Fetal Thymus	thymus
22	chr3:134072200-134082400	Genic enhancers	Brain Hippocampus Middle	brain
23	chr3:134072200-134090200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:134072400-134075600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:134072400-134076600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:134072400-134077200	Genic enhancers	Osteobl	bone
27	chr3:134072400-134091200	Genic enhancers	Spleen	Spleen
28	chr3:134072600-134075800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:134072600-134080200	Weak transcription	Small Intestine	intestine
30	chr3:134072600-134082000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:134072600-134082200	Genic enhancers	Adipose Nuclei	Adipose
32	chr3:134072800-134077000	Genic enhancers	NHEK	skin
33	chr3:134072800-134081000	Genic enhancers	Placenta Amnion	Placenta Amnion
34	chr3:134072800-134082400	Genic enhancers	Brain Cingulate Gyrus	brain
35	chr3:134072800-134082600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:134072800-134090600	Genic enhancers	Left Ventricle	heart
37	chr3:134073000-134075400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:134073000-134075400	Genic enhancers	HSMM	muscle
39	chr3:134073000-134075800	Strong transcription	Rectal Smooth Muscle	rectum
40	chr3:134073000-134076000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:134073000-134076200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:134073000-134076200	Genic enhancers	NHDF-Ad	bronchial
43	chr3:134073000-134076600	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr3:134073000-134077600	Transcr. at gene 5' and 3'	A549	lung
45	chr3:134073000-134078400	Genic enhancers	Fetal Kidney	kidney
46	chr3:134073000-134080400	Genic enhancers	Ovary	ovary
47	chr3:134073000-134082200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:134073000-134089400	Genic enhancers	HMEC	breast
49	chr3:134073200-134075400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:134073200-134075400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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