Variant report

Variant	rs1862130
Chromosome Location	chr5:154063778-154063779
allele	G/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	chr5:154063470-154064152	MCF-7	breast:	n/a	n/a
2	GATA3	chr5:154063398-154064100	MCF-7	breast:	n/a	n/a
3	JUN	chr5:154061777-154063927	K562	blood:	n/a	chr5:154062543-154062553 chr5:154062542-154062554 chr5:154062545-154062552 chr5:154062544-154062552 chr5:154062544-154062552
4	FOS	chr5:154062044-154063837	MCF10A-Er-Src	breast:	n/a	chr5:154062543-154062553 chr5:154062542-154062554 chr5:154062545-154062552 chr5:154062544-154062552 chr5:154062542-154062553 chr5:154062544-154062552
5	STAT3	chr5:154063762-154063782	MCF10A-Er-Src	breast:	n/a	n/a
6	GATA3	chr5:154063623-154063969	MCF-7	breast:	n/a	n/a
7	POLR2A	chr5:154063160-154063783	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:154059219..154066449-chr5:154131053..154139153,28	MCF-7	breast:
2	chr5:154032924..154035953-chr5:154060890..154064401,4	K562	blood:
3	chr5:154061087..154064928-chr5:154133720..154137511,10	MCF-7	breast:
4	chr5:154062083..154065077-chr5:154078214..154080372,2	K562	blood:
5	chr5:154053688..154055424-chr5:154062643..154064722,2	K562	blood:
6	chr5:154062466..154064358-chr5:154453743..154456113,2	K562	blood:
7	chr5:154062284..154064360-chr5:154130861..154133550,2	MCF-7	breast:
8	chr5:154061423..154063859-chr5:154072276..154076586,3	K562	blood:
9	chr5:154059571..154067369-chr5:154132796..154138140,13	K562	blood:
10	chr5:154061441..154064069-chr5:154090774..154094018,3	MCF-7	breast:
11	chr5:154061792..154064615-chr5:154236472..154239583,3	MCF-7	breast:
12	chr5:154062816..154065132-chr5:154065984..154069776,3	MCF-7	breast:
13	chr5:154060599..154064575-chr5:154133211..154138140,11	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LARP1-2	chr5:154062216-154065204	NONHSAT104706

Variant related genes	Relation type
MIR1303	TF binding region
ENSG00000170271	Chromatin interaction
ENSG00000155506	Chromatin interaction
ENSG00000155508	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1862131	0.83[EUR][1000 genomes]
rs1972618	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4958382	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958758	0.84[ASN][1000 genomes]
rs4958759	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4958760	0.83[EUR][1000 genomes]
rs4958761	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4958762	0.81[EUR][1000 genomes]
rs6580099	0.83[ASN][1000 genomes]
rs6580101	0.80[EUR][1000 genomes]
rs6580102	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580104	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7721183	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs918365	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs965235	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	nsv462491	chr5:154045280-154066205	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv600090	chr5:154045280-154066205	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154060800-154070000	Weak transcription	Gastric	stomach
2	chr5:154061600-154063800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:154062600-154063800	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr5:154062800-154064600	Enhancers	Esophagus	oesophagus
5	chr5:154063000-154063800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:154063000-154063800	Enhancers	Fetal Intestine Large	intestine
7	chr5:154063000-154064000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr5:154063000-154065600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:154063000-154069600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:154063200-154063800	Enhancers	HMEC	breast
11	chr5:154063200-154064000	Weak transcription	Left Ventricle	heart
12	chr5:154063200-154064200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:154063200-154064200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:154063200-154065000	Weak transcription	Fetal Intestine Small	intestine
15	chr5:154063200-154065200	Enhancers	Pancreas	Pancrea
16	chr5:154063400-154063800	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr5:154063400-154063800	Enhancers	Fetal Heart	heart
18	chr5:154063400-154063800	Enhancers	Rectal Smooth Muscle	rectum
19	chr5:154063400-154063800	Enhancers	GM12878-XiMat	blood
20	chr5:154063400-154064000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:154063400-154064000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr5:154063400-154064200	Enhancers	H9 Cell Line	embryonic stem cell
23	chr5:154063400-154064200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:154063400-154064200	Enhancers	Dnd41	blood
25	chr5:154063400-154064400	Weak transcription	Brain Angular Gyrus	brain
26	chr5:154063400-154064400	Enhancers	Psoas Muscle	Psoas
27	chr5:154063400-154064400	Enhancers	Hela-S3	cervix
28	chr5:154063400-154064600	Enhancers	Right Atrium	heart
29	chr5:154063400-154064800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr5:154063400-154065800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr5:154063600-154063800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:154063600-154063800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:154063600-154063800	Enhancers	Duodenum Mucosa	Duodenum
34	chr5:154063600-154063800	Enhancers	K562	blood
35	chr5:154063600-154063800	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr5:154063600-154064200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:154063600-154064400	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr5:154063600-154064600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr5:154063600-154065600	Weak transcription	A549	lung
40	chr5:154063600-154065800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr5:154063600-154066200	Enhancers	Liver	Liver
42	chr5:154063600-154066200	Weak transcription	Colonic Mucosa	Colon
43	chr5:154063600-154067200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:154063600-154069800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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