Variant report

Variant	rs2894179
Chromosome Location	chr6:31066671-31066672
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10947134	0.82[ASN][1000 genomes]
rs10947135	0.84[ASN][1000 genomes]
rs12527394	0.95[ASN][1000 genomes]
rs12529288	0.97[ASN][1000 genomes]
rs12662091	0.84[ASN][1000 genomes]
rs2233964	0.86[EUR][1000 genomes]
rs2233965	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2233970	0.84[ASN][1000 genomes]
rs2233973	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2233977	0.80[EUR][1000 genomes]
rs2233983	0.84[ASN][1000 genomes]
rs2233984	0.84[ASN][1000 genomes]
rs2233985	0.84[ASN][1000 genomes]
rs2394416	0.84[EUR][1000 genomes]
rs2394419	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2517473	0.84[ASN][1000 genomes]
rs34209658	0.96[ASN][1000 genomes]
rs35802713	0.96[ASN][1000 genomes]
rs3734854	0.84[ASN][1000 genomes]
rs4486065	0.89[EUR][1000 genomes]
rs4495304	0.81[ASN][1000 genomes]
rs4713431	0.95[ASN][1000 genomes]
rs4947246	0.88[ASN][1000 genomes]
rs4947296	0.97[ASN][1000 genomes]
rs4947297	0.96[ASN][1000 genomes]
rs4947299	0.92[ASN][1000 genomes]
rs4947302	0.88[ASN][1000 genomes]
rs9263460	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9263477	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9263499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9263508	0.82[EUR][1000 genomes]
rs9263509	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9263512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9263560	0.83[EUR][1000 genomes]
rs9263572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9263578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9263625	0.80[EUR][1000 genomes]
rs9295949	0.95[ASN][1000 genomes]
rs9295950	0.95[ASN][1000 genomes]
rs9295951	0.83[EUR][1000 genomes]
rs9348854	0.96[ASN][1000 genomes]
rs9357108	0.96[ASN][1000 genomes]
rs9380215	0.95[ASN][1000 genomes]
rs9380217	0.95[ASN][1000 genomes]
rs9391708	0.88[ASN][1000 genomes]
rs9391709	0.84[ASN][1000 genomes]
rs9394037	0.96[ASN][1000 genomes]
rs9394038	0.96[ASN][1000 genomes]
rs9405049	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv462746	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv601489	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2894179	ANKS1A	cis	cerebellum	SCAN
rs2894179	HIST1H1B	cis	cerebellum	SCAN
rs2894179	PACSIN1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31060800-31066800	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr6:31062800-31070000	Weak transcription	A549	lung
3	chr6:31063200-31070000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:31063200-31070000	Weak transcription	HMEC	breast
5	chr6:31065000-31066800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:31065000-31077600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:31065600-31069200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:31066200-31070000	Weak transcription	Lung	lung
9	chr6:31066400-31066800	Enhancers	K562	blood

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