Variant report

Variant	rs1972647
Chromosome Location	chr5:57556666-57556667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:57550054..57551732-chr5:57553774..57557457,3	K562	blood:
2	chr5:57482131..57485678-chr5:57554046..57557182,5	MCF-7	breast:
3	chr5:57551727..57557881-chr5:57751726..57757187,9	MCF-7	breast:
4	chr5:57555431..57557265-chr5:57747866..57749684,2	MCF-7	breast:
5	chr5:57554637..57557710-chr5:57746924..57749357,4	MCF-7	breast:
6	chr5:57555945..57557845-chr5:57750518..57752706,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145632	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1562242	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1862540	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2409006	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2910578	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2910579	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2910581	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2910586	0.84[EUR][1000 genomes]
rs2910606	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2962007	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2962025	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2964190	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2964192	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2964194	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2964196	0.89[AMR][1000 genomes]
rs2964197	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2964201	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs37489	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs37491	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs37511	0.82[AMR][1000 genomes]
rs37513	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs37514	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs37515	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs37517	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs37518	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs37525	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs37529	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs37530	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40531	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41385	0.81[ASN][1000 genomes]
rs466047	0.80[ASN][1000 genomes]
rs7715909	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs972060	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs972061	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[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	esv3489100	chr5:57545689-57669673	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3489101	chr5:57545689-57669673	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57552600-57557400	Weak transcription	Aorta	Aorta
2	chr5:57554400-57556800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:57554400-57557800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:57555600-57557000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr5:57555600-57558000	Enhancers	Fetal Heart	heart
6	chr5:57556000-57556800	Enhancers	NHLF	lung
7	chr5:57556000-57557000	Weak transcription	Fetal Lung	lung
8	chr5:57556000-57557400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:57556000-57557400	Weak transcription	Fetal Muscle Leg	muscle
10	chr5:57556000-57557400	Weak transcription	Left Ventricle	heart
11	chr5:57556000-57557400	Weak transcription	Right Atrium	heart
12	chr5:57556000-57557400	Weak transcription	HSMM	muscle
13	chr5:57556000-57557800	Enhancers	HUVEC	blood vessel
14	chr5:57556000-57558000	Enhancers	NHEK	skin
15	chr5:57556200-57556800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr5:57556200-57556800	Enhancers	HMEC	breast
17	chr5:57556200-57557200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:57556200-57557200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:57556200-57557400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:57556200-57557400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:57556200-57557400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:57556200-57557400	Weak transcription	HSMMtube	muscle
23	chr5:57556200-57558800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:57556400-57556800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:57556400-57557400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:57556400-57557400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:57556400-57557400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr5:57556400-57561200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:57556600-57557000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr5:57556600-57557000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:57556600-57557000	Weak transcription	NH-A	brain
32	chr5:57556600-57557000	Weak transcription	NHDF-Ad	bronchial
33	chr5:57556600-57557000	Weak transcription	Osteobl	bone
34	chr5:57556600-57558200	Enhancers	A549	lung

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