Variant report

Variant	rs2167530
Chromosome Location	chr2:134393846-134393847
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	chr2:134393103..134394680-chr2:134395761..134398691,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10174467	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10200864	0.88[ASN][1000 genomes]
rs13382906	0.91[ASN][1000 genomes]
rs13402567	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13418989	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13419711	0.89[ASN][1000 genomes]
rs1614797	0.86[ASN][1000 genomes]
rs1622528	0.87[ASN][1000 genomes]
rs1653790	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1653791	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1653792	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1653794	0.86[ASN][1000 genomes]
rs1669465	0.86[ASN][1000 genomes]
rs1669469	0.84[ASN][1000 genomes]
rs1901431	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1901451	0.88[ASN][1000 genomes]
rs1901452	0.90[ASN][1000 genomes]
rs4362615	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61112423	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6430435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758320	0.82[ASN][1000 genomes]
rs73000199	0.91[ASN][1000 genomes]
rs7569801	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7586760	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7599633	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv431713	chr2:134316522-134413604	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1013713	chr2:134322236-134644574	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv535931	chr2:134322236-134644574	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv2934	chr2:134368478-134412454	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv998920	chr2:134382097-134424640	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2167530	CHKA	trans	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134389800-134394400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:134392000-134394000	Enhancers	Brain Hippocampus Middle	brain
3	chr2:134392000-134394000	Enhancers	Fetal Heart	heart
4	chr2:134392000-134394200	Enhancers	NHEK	skin
5	chr2:134392000-134396600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:134392000-134397800	Weak transcription	Brain Angular Gyrus	brain
7	chr2:134392200-134394400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:134392200-134395600	Enhancers	Brain Substantia Nigra	brain
9	chr2:134392200-134396600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:134392200-134397200	Weak transcription	HMEC	breast
11	chr2:134392200-134398400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:134392200-134398800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:134392800-134399000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:134393000-134394400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:134393000-134394400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:134393000-134397000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:134393800-134394400	Enhancers	Brain Anterior Caudate	brain

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