Variant report

Variant	rs1552487
Chromosome Location	chr3:157504375-157504376
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:157497127..157499072-chr3:157502852..157504672,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10222405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10446283	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10446335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936108	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11709138	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11712832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552486	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1685679	0.98[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1685680	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1872981	0.98[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1979577	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979578	0.99[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1994480	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054862	0.99[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2054863	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054864	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3045100	0.83[ASN][1000 genomes]
rs3845979	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7630713	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs792738	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs792739	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs792740	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs807201	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs809395	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs901820	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809803	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816230	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833772	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836369	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837419	0.95[ASN][1000 genomes]
rs9847213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9867271	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876088	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9882048	0.87[EUR][1000 genomes];0.94[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	nsv592121	chr3:157437068-157593470	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv997770	chr3:157441619-157595315	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157501800-157504800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:157501800-157504800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:157502200-157505800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:157502200-157508200	Enhancers	HMEC	breast
5	chr3:157502400-157504800	Enhancers	Hela-S3	cervix
6	chr3:157502400-157505200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:157502400-157505600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:157502600-157504600	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr3:157502600-157504600	Enhancers	Rectal Smooth Muscle	rectum
10	chr3:157502600-157505000	Enhancers	NH-A	brain
11	chr3:157502600-157505200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:157502600-157505200	Enhancers	NHLF	lung
13	chr3:157502600-157508000	Enhancers	NHEK	skin
14	chr3:157502800-157504400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:157502800-157504800	Enhancers	HSMM	muscle
16	chr3:157502800-157505000	Enhancers	Adipose Nuclei	Adipose
17	chr3:157503000-157504400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:157503000-157504600	Enhancers	Fetal Stomach	stomach
19	chr3:157503400-157504400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:157503400-157504400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:157503400-157504400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:157503400-157504400	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:157503400-157504400	Weak transcription	Ovary	ovary
24	chr3:157503400-157504400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:157503400-157504800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:157503400-157505200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr3:157503400-157505200	Enhancers	Osteobl	bone
28	chr3:157503800-157504600	Weak transcription	HSMMtube	muscle
29	chr3:157504000-157504400	Active TSS	A549	lung
30	chr3:157504000-157504400	Enhancers	NHDF-Ad	bronchial
31	chr3:157504000-157504600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:157504000-157505000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:157504000-157505000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:157504000-157505200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:157504000-157505200	Enhancers	Aorta	Aorta
36	chr3:157504200-157504800	Enhancers	Fetal Muscle Leg	muscle

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