Variant report

Variant	rs59481688
Chromosome Location	chr1:225789833-225789834
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225788261..225790138-chr1:225790490..225792090,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11801322	0.90[AFR][1000 genomes]
rs11808089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617210	0.85[AFR][1000 genomes]
rs57616580	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58221350	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58384340	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60271197	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60588592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426081	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687755	0.98[AFR][1000 genomes]
rs6687947	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696683	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702446	1.00[ASN][1000 genomes]
rs73124025	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73125705	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73125706	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515673	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531033	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555097	0.93[AMR][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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225748800-225799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:225768800-225805600	Weak transcription	Aorta	Aorta
4	chr1:225774800-225793200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:225776400-225797200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:225777000-225793400	Weak transcription	Pancreas	Pancrea
7	chr1:225778600-225794200	Weak transcription	Brain Substantia Nigra	brain
8	chr1:225780200-225790400	Weak transcription	NHLF	lung
9	chr1:225780200-225794200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:225780800-225815400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:225781000-225791400	Weak transcription	Adipose Nuclei	Adipose
12	chr1:225781000-225825400	Weak transcription	Fetal Stomach	stomach
13	chr1:225781200-225793200	Weak transcription	Ovary	ovary
14	chr1:225782000-225791200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:225782000-225795000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:225782400-225795200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:225782400-225806200	Weak transcription	Right Ventricle	heart
18	chr1:225783400-225790400	Weak transcription	NH-A	brain
19	chr1:225784000-225790600	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:225784200-225790200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:225784200-225791400	Weak transcription	Fetal Lung	lung
22	chr1:225784200-225807800	Weak transcription	Fetal Brain Male	brain
23	chr1:225784400-225791600	Weak transcription	HSMMtube	muscle
24	chr1:225784800-225790400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:225784800-225791200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:225784800-225793200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:225785000-225790800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:225785200-225800000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:225785400-225790400	Weak transcription	HMEC	breast
30	chr1:225785400-225794600	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:225785800-225790200	Weak transcription	Brain Anterior Caudate	brain
32	chr1:225785800-225790200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:225785800-225790400	Weak transcription	HSMM	muscle
34	chr1:225786200-225790400	Weak transcription	NHEK	skin
35	chr1:225786400-225790200	Weak transcription	Osteobl	bone
36	chr1:225787000-225790400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:225787200-225790200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:225787400-225790200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:225787800-225794600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:225788000-225791400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:225788000-225793000	Weak transcription	Fetal Intestine Small	intestine
42	chr1:225788400-225790400	Weak transcription	Brain Angular Gyrus	brain
43	chr1:225788400-225790800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:225788400-225795000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:225788400-225795200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:225788400-225796200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr1:225788600-225791200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:225788600-225794800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:225789000-225790400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:225789400-225792200	Enhancers	Hela-S3	cervix

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