Variant report

Variant	rs289677
Chromosome Location	chr1:76560709-76560710
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	chr1:76559480..76561053-chr1:76563523..76565127,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12408886	1.00[JPT][hapmap]
rs12408918	1.00[JPT][hapmap]
rs158620	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17098119	1.00[JPT][hapmap]
rs190861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2631779	1.00[JPT][hapmap]
rs289674	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289676	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289687	1.00[JPT][hapmap]
rs289692	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289693	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs291059	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35802431	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs384233	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs403449	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs409245	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs447383	0.88[EUR][1000 genomes]
rs491409	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs50564	0.81[YRI][hapmap]
rs551954	0.93[EUR][1000 genomes]
rs552890	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588073	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs61558985	0.89[EUR][1000 genomes]
rs6673424	1.00[JPT][hapmap]

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	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv871862	chr1:76525783-76598209	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76542800-76572000	Weak transcription	Primary B cells from cord blood	blood
2	chr1:76548000-76561800	Weak transcription	Fetal Brain Female	brain
3	chr1:76548400-76576200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:76556800-76561400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:76557000-76561400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:76557400-76561600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:76557400-76561600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:76557400-76605800	Weak transcription	Fetal Intestine Small	intestine
9	chr1:76557600-76561400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:76557600-76561400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:76557600-76588800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:76558400-76562000	Enhancers	Brain Substantia Nigra	brain
13	chr1:76559000-76562000	Enhancers	Brain Cingulate Gyrus	brain
14	chr1:76559600-76560800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:76559600-76562200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr1:76559600-76566800	Weak transcription	Fetal Lung	lung
17	chr1:76559800-76560800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:76560000-76561000	Weak transcription	Fetal Kidney	kidney
19	chr1:76560000-76561200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:76560000-76561600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:76560000-76571000	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:76560200-76573400	Weak transcription	Brain Angular Gyrus	brain
23	chr1:76560600-76561200	Weak transcription	Brain Anterior Caudate	brain

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