Variant report

Variant	rs7539051
Chromosome Location	chr1:57042954-57042955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:56968634..56970634-chr1:57041979..57044955,2	MCF-7	breast:
2	chr1:56941233..56944264-chr1:57041554..57045074,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11206845	0.84[AFR][1000 genomes]
rs11206846	0.94[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11206847	0.82[AFR][1000 genomes]
rs11800865	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11800883	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11810635	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12024140	0.81[CHB][hapmap]
rs12058536	0.84[AFR][1000 genomes]
rs12059747	0.90[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs12059843	0.84[AFR][1000 genomes]
rs12070247	0.90[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs12070557	0.84[AFR][1000 genomes]
rs12090895	0.84[AFR][1000 genomes]
rs12098117	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs1418521	0.81[MKK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs1572058	1.00[ASW][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28673510	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41446844	0.90[ASW][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56332336	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6661359	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6699960	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6702052	0.84[AFR][1000 genomes]
rs72664373	0.96[ASN][1000 genomes]
rs72664400	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72903425	0.84[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57038000-57043400	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr1:57038000-57043800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:57038400-57043200	Weak transcription	Spleen	Spleen
4	chr1:57039600-57043200	Active TSS	NHLF	lung
5	chr1:57039600-57046000	Active TSS	Right Atrium	heart
6	chr1:57040000-57045600	Active TSS	Brain Angular Gyrus	brain
7	chr1:57040000-57046000	Active TSS	Ovary	ovary
8	chr1:57040200-57043400	Active TSS	Placenta	Placenta
9	chr1:57040200-57043600	Active TSS	Fetal Muscle Trunk	muscle
10	chr1:57040200-57043800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:57040200-57044200	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr1:57040200-57045800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr1:57040200-57046000	Active TSS	Right Ventricle	heart
14	chr1:57040400-57045600	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr1:57040600-57043800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:57040600-57045600	Active TSS	Brain Cingulate Gyrus	brain
17	chr1:57040800-57044000	Flanking Active TSS	HUVEC	blood vessel
18	chr1:57040800-57045600	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr1:57040800-57045800	Active TSS	Placenta Amnion	Placenta Amnion
20	chr1:57041000-57045600	Active TSS	H1 Cell Line	embryonic stem cell
21	chr1:57041000-57045800	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr1:57041200-57045600	Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:57041200-57045600	Active TSS	Aorta	Aorta
24	chr1:57041400-57043000	Active TSS	HepG2	liver
25	chr1:57041400-57045600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:57041400-57045600	Active TSS	Liver	Liver
27	chr1:57041600-57043200	Active TSS	Fetal Stomach	stomach
28	chr1:57041600-57045400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr1:57041800-57043000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:57041800-57045600	Active TSS	Brain Hippocampus Middle	brain
31	chr1:57041800-57046000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:57042000-57043200	Enhancers	Primary hematopoietic stem cells	blood
33	chr1:57042000-57043600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr1:57042000-57045600	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr1:57042000-57045600	Active TSS	Fetal Intestine Large	intestine
36	chr1:57042000-57045800	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr1:57042200-57043000	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr1:57042200-57043400	Flanking Active TSS	Thymus	Thymus
39	chr1:57042200-57043600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr1:57042200-57043800	Enhancers	Fetal Heart	heart
41	chr1:57042200-57044200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr1:57042200-57045800	Active TSS	Left Ventricle	heart
43	chr1:57042400-57043000	Active TSS	Colon Smooth Muscle	Colon
44	chr1:57042400-57043000	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr1:57042400-57043000	Flanking Active TSS	Fetal Kidney	kidney
46	chr1:57042400-57043000	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr1:57042400-57043000	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr1:57042400-57043200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:57042400-57043400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:57042400-57043400	Active TSS	Brain Germinal Matrix	brain

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