Variant report

Variant	rs2841549
Chromosome Location	chr6:13489554-13489555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11759779	0.92[ASN][1000 genomes]
rs2115063	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.97[ASN][1000 genomes]
rs2560761	0.84[CHB][hapmap]
rs2560789	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs2560790	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs2841548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715379	0.85[CEU][hapmap]
rs6458872	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458898	0.85[CEU][hapmap]
rs7758810	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9367502	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370156	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382154	0.92[CEU][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.89[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv462640	chr6:13426539-13519434	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv600994	chr6:13426539-13519434	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv470802	chr6:13441424-13519371	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3421701	chr6:13485573-13489871	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2841549	GFOD1	cis	cerebellum	SCAN
rs2841549	C6orf52	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13485000-13489600	Active TSS	Rectal Smooth Muscle	rectum
2	chr6:13488400-13494400	Weak transcription	HSMMtube	muscle
3	chr6:13488600-13490200	Weak transcription	NHDF-Ad	bronchial
4	chr6:13488800-13489600	Enhancers	Right Ventricle	heart
5	chr6:13489000-13489600	Enhancers	Esophagus	oesophagus
6	chr6:13489000-13489600	Enhancers	Right Atrium	heart
7	chr6:13489000-13489600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr6:13489000-13490800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:13489000-13494200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:13489200-13489600	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr6:13489200-13490600	Weak transcription	Placenta	Placenta
12	chr6:13489200-13496600	Weak transcription	Spleen	Spleen
13	chr6:13489200-13496600	Weak transcription	GM12878-XiMat	blood
14	chr6:13489400-13489600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:13489400-13493800	Weak transcription	Adipose Nuclei	Adipose
16	chr6:13489400-13494000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:13489400-13494200	Weak transcription	Fetal Heart	heart
18	chr6:13489400-13495600	Weak transcription	Left Ventricle	heart

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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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