Variant report

Variant	rs12317
Chromosome Location	chr3:134074730-134074731
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr3:134074479-134075011	A549	lung:	n/a	n/a
2	FOXA2	chr3:134074672-134075065	A549	lung:	n/a	n/a
3	POLR2A	chr3:134071448-134074783	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr3:134071878-134074839	HUVEC	blood vessel:	n/a	n/a
5	FOXA1	chr3:134074596-134075022	T-47D	breast:	n/a	chr3:134074803-134074818
6	POLR2A	chr3:134071177-134074761	H1-hESC	embryonic stem cell:	n/a	n/a
7	CHD1	chr3:134070900-134094634	IMR90	lung:	n/a	chr3:134093783-134093793 chr3:134092557-134092567 chr3:134083055-134083065
8	POLR2A	chr3:134071087-134094366	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:134071303-134093679	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:134071236-134074903	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr3:134071113-134074862	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr3:134071260-134074834	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr3:134071435-134074901	PANC-1	pancreas:	n/a	n/a
14	FOXA1	chr3:134074642-134074885	T-47D	breast:	n/a	chr3:134074803-134074818
15	POLR2A	chr3:134069255-134074808	A549	lung:	n/a	n/a
16	POLR2A	chr3:134072288-134074859	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr3:134074602-134074790	ProgFib	skin:	n/a	n/a
18	POLR2A	chr3:134069355-134094620	IMR90	lung:	n/a	n/a

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:

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

Extended variants
information (count: 3 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs1077718	1.00[AFR][1000 genomes];0.80[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

No data

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	chr3:134070400-134075000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:134070400-134075000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:134070400-134088200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:134071000-134075800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:134071000-134082600	Genic enhancers	NHLF	lung
13	chr3:134071000-134088800	Enhancers	Right Atrium	heart
14	chr3:134071200-134082400	Genic enhancers	Brain Substantia Nigra	brain
15	chr3:134071400-134075200	Strong transcription	Aorta	Aorta
16	chr3:134071400-134079000	Genic enhancers	Fetal Intestine Large	intestine
17	chr3:134071600-134076000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:134071600-134076400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:134071600-134082200	Weak transcription	Primary T cells from cord blood	blood
20	chr3:134071600-134082800	Genic enhancers	Placenta	Placenta
21	chr3:134071800-134075400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:134072000-134079000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:134072000-134082800	Genic enhancers	Lung	lung
24	chr3:134072200-134076600	Weak transcription	Fetal Thymus	thymus
25	chr3:134072200-134082400	Genic enhancers	Brain Hippocampus Middle	brain
26	chr3:134072200-134090200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:134072400-134075600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:134072400-134076600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:134072400-134077200	Genic enhancers	Osteobl	bone
30	chr3:134072400-134091200	Genic enhancers	Spleen	Spleen
31	chr3:134072600-134075200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:134072600-134075800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:134072600-134080200	Weak transcription	Small Intestine	intestine
34	chr3:134072600-134082000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:134072600-134082200	Genic enhancers	Adipose Nuclei	Adipose
36	chr3:134072800-134075200	Genic enhancers	HSMMtube	muscle
37	chr3:134072800-134077000	Genic enhancers	NHEK	skin
38	chr3:134072800-134081000	Genic enhancers	Placenta Amnion	Placenta Amnion
39	chr3:134072800-134082400	Genic enhancers	Brain Cingulate Gyrus	brain
40	chr3:134072800-134082600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:134072800-134090600	Genic enhancers	Left Ventricle	heart
42	chr3:134073000-134075400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:134073000-134075400	Genic enhancers	HSMM	muscle
44	chr3:134073000-134075800	Strong transcription	Rectal Smooth Muscle	rectum
45	chr3:134073000-134076000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:134073000-134076200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:134073000-134076200	Genic enhancers	NHDF-Ad	bronchial
48	chr3:134073000-134076600	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr3:134073000-134077600	Transcr. at gene 5' and 3'	A549	lung
50	chr3:134073000-134078400	Genic enhancers	Fetal Kidney	kidney

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