Variant report

Variant	rs62278056
Chromosome Location	chr3:160942363-160942364
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	GATA3	chr3:160941970-160943186	MCF-7	breast:	n/a	chr3:160943048-160943061
2	POLR2A	chr3:160941329-160943182	MCF-7	breast:	n/a	n/a
3	GATA3	chr3:160942335-160942821	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
2	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
3	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
4	chr3:160940674..160943053-chr3:161145134..161148083,2	MCF-7	breast:
5	chr3:160940058..160942666-chr3:161042036..161044035,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271052	TF binding region
NMD3	TF binding region
ENSG00000169255	Chromatin interaction
ENSG00000269888	Chromatin interaction
ENSG00000234851	Chromatin interaction
ENSG00000240138	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs16832063	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16832129	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16847274	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62278032	1.00[AMR][1000 genomes]
rs62278054	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62278057	0.82[EUR][1000 genomes]
rs62279886	0.84[AMR][1000 genomes]
rs62279918	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62279920	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62279922	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62279923	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62279924	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62279925	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62279927	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62279929	0.89[AMR][1000 genomes]
rs62279930	0.89[AMR][1000 genomes]
rs62279931	0.89[AMR][1000 genomes]
rs62279948	0.89[AMR][1000 genomes]
rs62279949	0.89[AMR][1000 genomes]
rs62279950	0.89[AMR][1000 genomes]
rs73162552	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73162554	0.89[AMR][1000 genomes];0.83[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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160938600-160942400	Active TSS	Right Ventricle	heart
2	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:160940000-160942400	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr3:160940000-160971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:160940000-160977400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:160940200-160942800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:160940200-160943800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:160940200-160965400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:160940400-160943000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr3:160940800-160942800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:160940800-160946600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:160940800-160946600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:160940800-160956000	Weak transcription	Colonic Mucosa	Colon
14	chr3:160941000-160942400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:160941000-160942400	Weak transcription	Primary B cells from cord blood	blood
16	chr3:160941000-160942400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr3:160941000-160942600	Transcr. at gene 5' and 3'	Osteobl	bone
18	chr3:160941000-160942800	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:160941000-160942800	Weak transcription	NHDF-Ad	bronchial
20	chr3:160941000-160943400	Active TSS	GM12878-XiMat	blood
21	chr3:160941000-160943800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:160941000-160946400	Weak transcription	Brain Substantia Nigra	brain
23	chr3:160941000-160946400	Weak transcription	Lung	lung
24	chr3:160941000-160946400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:160941000-160946600	Weak transcription	Thymus	Thymus
26	chr3:160941000-160956000	Weak transcription	Esophagus	oesophagus
27	chr3:160941000-160969600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:160941000-160970200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:160941000-160974800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:160941000-160983000	Weak transcription	Spleen	Spleen
31	chr3:160941000-160984600	Weak transcription	Small Intestine	intestine
32	chr3:160941000-160993400	Weak transcription	Pancreas	Pancrea
33	chr3:160941200-160942400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr3:160941200-160942400	Weak transcription	Left Ventricle	heart
35	chr3:160941200-160942600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr3:160941200-160942600	Weak transcription	Fetal Thymus	thymus
37	chr3:160941200-160942800	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr3:160941200-160942800	Weak transcription	Ovary	ovary
39	chr3:160941200-160943000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr3:160941200-160943400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:160941200-160943800	Weak transcription	Aorta	Aorta
42	chr3:160941200-160944800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:160941200-160945800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:160941200-160946000	Weak transcription	HSMMtube	muscle
45	chr3:160941200-160946400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:160941200-160946800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:160941200-160968600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr3:160941200-160969800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:160941200-160973400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:160941400-160942400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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