Variant report

Variant	rs12208211
Chromosome Location	chr6:26565560-26565561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26536222..26540133-chr6:26565164..26569470,5	K562	blood:
2	chr6:26563515..26565648-chr6:27059031..27061634,2	K562	blood:

Variant related genes	Relation type
ENSG00000182952	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10447390	0.86[CEU][hapmap]
rs10447391	0.86[CEU][hapmap]
rs10456047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10456331	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10484441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10807008	1.00[CEU][hapmap]
rs10946820	0.86[CEU][hapmap]
rs10946821	0.86[CEU][hapmap]
rs10946823	0.92[CEU][hapmap]
rs10946824	0.86[CEU][hapmap]
rs10946825	0.91[CEU][hapmap]
rs10946826	0.86[CEU][hapmap]
rs10946827	0.85[CEU][hapmap]
rs10946829	0.86[CEU][hapmap]
rs10946832	1.00[CEU][hapmap]
rs10946842	1.00[JPT][hapmap]
rs1131936	0.93[CEU][hapmap]
rs12191917	0.86[CEU][hapmap]
rs12193283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12194001	0.83[CEU][hapmap]
rs12194036	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12194073	0.86[CEU][hapmap]
rs12196371	1.00[CEU][hapmap]
rs12197304	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12198993	0.86[CEU][hapmap]
rs12201546	0.86[CEU][hapmap]
rs12205310	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12206812	0.86[CEU][hapmap]
rs12207930	0.86[CEU][hapmap]
rs12208272	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12208788	0.93[CEU][hapmap]
rs12211872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12214444	1.00[CEU][hapmap]
rs12214486	0.86[CEU][hapmap]
rs12214924	0.86[CEU][hapmap]
rs12661560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12664899	0.93[CEU][hapmap]
rs17537465	0.93[CEU][hapmap]
rs17539219	0.86[CEU][hapmap]
rs17610161	1.00[CEU][hapmap]
rs17611220	0.86[CEU][hapmap]
rs17611438	0.85[CEU][hapmap]
rs1884945	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2393652	0.86[CEU][hapmap]
rs2393664	0.81[CEU][hapmap]
rs2893844	0.85[CEU][hapmap]
rs2893845	0.86[CEU][hapmap]
rs2893847	0.86[CEU][hapmap]
rs2893848	0.86[CEU][hapmap]
rs2893849	0.93[CEU][hapmap]
rs2893856	0.93[CEU][hapmap]
rs2893857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3198487	0.85[CEU][hapmap]
rs3208734	0.85[CEU][hapmap]
rs3757143	1.00[YRI][hapmap]
rs3846843	0.86[CEU][hapmap]
rs3846844	0.86[CEU][hapmap]
rs3846847	0.86[CEU][hapmap]
rs3846848	0.86[CEU][hapmap]
rs3846849	0.86[CEU][hapmap]
rs3902051	0.93[CEU][hapmap]
rs4083469	0.86[CEU][hapmap]
rs4609015	0.86[CEU][hapmap]
rs4711108	1.00[CEU][hapmap]
rs4711109	0.86[CEU][hapmap]
rs4711110	1.00[CEU][hapmap]
rs4711111	0.86[CEU][hapmap]
rs4712986	0.93[CEU][hapmap]
rs4712988	0.93[CEU][hapmap]
rs4712990	1.00[CEU][hapmap]
rs4712993	0.86[CEU][hapmap]
rs4712994	0.86[CEU][hapmap]
rs4712996	0.86[CEU][hapmap]
rs4712999	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs4713000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713011	1.00[JPT][hapmap]
rs56034653	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456722	0.85[CEU][hapmap]
rs6456724	0.93[CEU][hapmap]
rs6900725	0.86[CEU][hapmap]
rs6901245	0.84[CEU][hapmap]
rs6910023	0.86[CEU][hapmap]
rs6912934	0.93[CEU][hapmap]
rs6920986	0.86[CEU][hapmap]
rs6926878	0.86[CEU][hapmap]
rs6928454	0.86[CEU][hapmap]
rs6929846	0.86[CEU][hapmap]
rs72843766	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7355	0.93[CEU][hapmap]
rs7356849	0.93[CEU][hapmap]
rs7744254	0.86[CEU][hapmap]
rs7745238	0.86[CEU][hapmap]
rs7745767	0.86[CEU][hapmap]
rs7751280	0.86[CEU][hapmap]
rs7768108	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs7770214	0.86[CEU][hapmap]
rs882010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295690	0.81[CEU][hapmap]
rs9467759	0.93[CEU][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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12208211	GMNN	cis	parietal	SCAN
rs12208211	OR4K14	trans	parietal	SCAN
rs12208211	BTN2A1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26557400-26568400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:26559600-26568200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:26562000-26568400	Weak transcription	Aorta	Aorta
4	chr6:26562200-26568000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:26562200-26568400	Weak transcription	Pancreas	Pancrea
6	chr6:26564400-26568200	Weak transcription	Dnd41	blood
7	chr6:26565200-26568000	Weak transcription	K562	blood
8	chr6:26565400-26565600	Flanking Active TSS	HepG2	liver

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