Variant report

Variant	rs1317554
Chromosome Location	chr3:133178432-133178433
allele	C/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	POLR2A	chr3:133178162-133178579	PFSK-1	brain:	n/a	n/a
2	GATA3	chr3:133178119-133178606	T-47D	breast:	n/a	n/a
3	GATA3	chr3:133178152-133178579	T-47D	breast:	n/a	n/a
4	REST	chr3:133178199-133178461	PFSK-1	brain:	n/a	chr3:133178434-133178447
5	FOXA1	chr3:133178219-133178652	T-47D	breast:	n/a	n/a
6	FOXA1	chr3:133178217-133178560	T-47D	breast:	n/a	n/a
7	TCF7L2	chr3:133177631-133178713	PANC-1	pancreas:	n/a	chr3:133177802-133177811
8	EP300	chr3:133178080-133178797	T-47D	breast:	n/a	chr3:133178208-133178222 chr3:133178583-133178596
9	POLR2A	chr3:133178090-133178633	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:133169398..133190840-chr3:133288286..133298861,41	MCF-7	breast:
2	chr3:133167608..133169678-chr3:133177159..133179764,2	MCF-7	breast:
3	chr3:133161498..133163430-chr3:133177580..133180492,2	MCF-7	breast:
4	chr3:133175597..133178522-chr3:133290456..133293347,3	MCF-7	breast:

Variant related genes	Relation type
BFSP2-AS1	TF binding region
ENSG00000170819	Chromatin interaction
ENSG00000091527	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1610172	0.83[ASN][1000 genomes]
rs7645387	0.83[ASN][1000 genomes]
rs967651	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007047	chr3:133137664-133181388	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1006289	chr3:133137664-133186808	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv1829199	chr3:133158065-133213047	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv877505	chr3:133167363-133235272	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv237800	chr3:133178030-133185521	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133161000-133191000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:133165400-133178600	Weak transcription	Aorta	Aorta
3	chr3:133168200-133178800	Weak transcription	Fetal Kidney	kidney
4	chr3:133169800-133179400	Weak transcription	GM12878-XiMat	blood
5	chr3:133175000-133178800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:133175000-133179600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:133176200-133178600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:133177200-133185800	Enhancers	Fetal Thymus	thymus
9	chr3:133177400-133180600	Enhancers	Thymus	Thymus
10	chr3:133177600-133181600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:133177800-133178600	Enhancers	A549	lung
12	chr3:133177800-133179000	Enhancers	Liver	Liver
13	chr3:133177800-133179200	Enhancers	Colon Smooth Muscle	Colon
14	chr3:133177800-133179600	Enhancers	Esophagus	oesophagus
15	chr3:133177800-133180000	Enhancers	Fetal Stomach	stomach
16	chr3:133178000-133179000	Enhancers	Stomach Smooth Muscle	stomach
17	chr3:133178000-133180800	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr3:133178200-133178600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:133178200-133178600	Enhancers	Fetal Muscle Trunk	muscle
20	chr3:133178200-133178600	Enhancers	Left Ventricle	heart
21	chr3:133178200-133178600	Enhancers	Ovary	ovary
22	chr3:133178200-133178600	Enhancers	Right Ventricle	heart
23	chr3:133178200-133179000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:133178200-133179000	Enhancers	Fetal Lung	lung
25	chr3:133178200-133179600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:133178200-133180000	Enhancers	Adipose Nuclei	Adipose
27	chr3:133178200-133180000	Enhancers	Psoas Muscle	Psoas
28	chr3:133178200-133180000	Enhancers	Right Atrium	heart
29	chr3:133178200-133180400	Enhancers	Fetal Muscle Leg	muscle
30	chr3:133178200-133180600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr3:133178200-133181000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:133178200-133181400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:133178400-133178600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr3:133178400-133178600	Bivalent Enhancer	NHLF	lung
35	chr3:133178400-133178800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:133178400-133178800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:133178400-133178800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr3:133178400-133178800	Enhancers	Brain Hippocampus Middle	brain
39	chr3:133178400-133178800	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr3:133178400-133178800	Enhancers	HepG2	liver
41	chr3:133178400-133179400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:133178400-133180000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:133178400-133180000	Enhancers	Colonic Mucosa	Colon
44	chr3:133178400-133180000	Enhancers	Placenta	Placenta
45	chr3:133178400-133180000	Enhancers	Stomach Mucosa	stomach
46	chr3:133178400-133180600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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