Variant report

Variant	rs980644
Chromosome Location	chr2:54984424-54984425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1510614	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1813272	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1848924	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1848925	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2116441	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288682	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288683	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671972	0.85[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs980644	EML6	cis	Thyroid	GTEx
rs980644	CCDC85A	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54982200-54986400	Enhancers	Primary B cells from peripheral blood	blood
2	chr2:54983000-54984800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:54983400-54984600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr2:54983400-54984600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:54983400-54984800	Enhancers	GM12878-XiMat	blood
6	chr2:54983600-54984600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:54983600-54984600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:54983600-54984600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:54983600-54984600	Weak transcription	NHEK	skin
10	chr2:54983600-54985600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:54983600-54991600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:54983800-54985800	Enhancers	Primary B cells from cord blood	blood
13	chr2:54984200-54985600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr2:54984400-54984600	Enhancers	Thymus	Thymus
15	chr2:54984400-54985000	Enhancers	NH-A	brain
16	chr2:54984400-54985600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr2:54984400-54985600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:54984400-54985800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr2:54984400-54985800	Enhancers	Brain Anterior Caudate	brain

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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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