Variant report

Variant	rs2205829
Chromosome Location	chr6:27480227-27480228
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1011665	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs12529458	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[YRI][hapmap]
rs12529756	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12663650	0.90[CEU][hapmap]
rs12664996	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs13220817	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs1883403	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs2064093	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs2235232	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2393962	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2393963	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393964	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4711154	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711155	0.91[ASN][1000 genomes]
rs6913166	0.98[GIH][hapmap];0.87[MEX][hapmap]
rs6914864	0.87[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs7761966	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs9393813	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]

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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv462665	chr6:27458013-27547792	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv601203	chr6:27458013-27547792	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2205829	ZNF391	cis	lung	GTEx
rs2205829	ZNF391	cis	parietal	SCAN
rs2205829	ZNF391	cis	Skin Sun Exposed Lower leg	GTEx
rs2205829	ZNF391	cis	cerebellum	SCAN
rs2205829	BTN3A2	cis	cerebellum	SCAN
rs2205829	HIST1H2AJ	cis	cerebellum	SCAN
rs2205829	ZNF204P	cis	parietal	SCAN
rs2205829	ZNF391	cis	Esophagus Muscularis	GTEx
rs2205829	ZSCAN23	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27475400-27482400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:27475400-27482600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:27479000-27481000	Weak transcription	K562	blood
4	chr6:27480000-27480400	Enhancers	H1 Cell Line	embryonic stem cell
5	chr6:27480000-27480400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:27480200-27482200	Weak transcription	H9 Cell Line	embryonic stem cell

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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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