Variant report

Variant	rs993541
Chromosome Location	chr2:55078197-55078198
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10188555	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12713278	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13033668	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13033818	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2165006	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545449	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7574117	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7596552	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv1844727	chr2:54999712-55084583	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv874154	chr2:55063113-55084583	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv457930	chr2:55073428-55091029	Weak transcription Enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv582028	chr2:55073428-55091029	Enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55053400-55079000	Weak transcription	HepG2	liver
2	chr2:55066800-55084400	Weak transcription	HSMMtube	muscle
3	chr2:55066800-55088800	Weak transcription	Brain Substantia Nigra	brain
4	chr2:55068400-55096200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:55068400-55109000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:55068600-55122400	Weak transcription	Brain Anterior Caudate	brain
7	chr2:55072600-55091600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:55073400-55080400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:55073400-55093800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr2:55077200-55078200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:55077200-55078200	Enhancers	NHEK	skin
12	chr2:55078000-55082400	Weak transcription	HMEC	breast
13	chr2:55078000-55086400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:55078000-55087600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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