Variant report

Variant	rs17268697
Chromosome Location	chr6:25758448-25758449
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25756144..25758760-chr6:25767173..25770063,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1359231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17269374	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17271121	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap]
rs17320558	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17492659	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2154217	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2186087	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2328892	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41271827	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4145220	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4236036	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs4395714	0.88[EUR][1000 genomes]
rs45493498	0.86[EUR][1000 genomes]
rs57053773	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59537771	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62392667	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62392668	0.86[EUR][1000 genomes]
rs62392670	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62392671	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62392673	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62392674	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62392676	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62392694	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62392695	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62392696	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62392731	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62392732	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62392734	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62392736	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62392752	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62392756	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62392759	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62393720	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62394267	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62394268	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62394270	0.86[EUR][1000 genomes]
rs72840306	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72840350	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72843538	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9461202	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv427747	chr6:25641380-25908218	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv969355	chr6:25733459-25779530	Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17268697	GPX6	cis	parietal	SCAN
rs17268697	BTN3A2	cis	cerebellum	SCAN
rs17268697	HIST1H2AB	cis	cerebellum	SCAN
rs17268697	SLC17A1	cis	multi-tissue	Pritchard
rs17268697	SLC17A1	cis	Liver	GTEx
rs17268697	HFE	cis	cerebellum	SCAN
rs17268697	ZKSCAN3	cis	parietal	SCAN
rs17268697	HIST1H2BH	cis	cerebellum	SCAN
rs17268697	OR2B2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25754600-25760000	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr6:25756000-25758600	Flanking Active TSS	Liver	Liver
3	chr6:25757000-25758600	Enhancers	Fetal Intestine Large	intestine
4	chr6:25758000-25758600	ZNF genes & repeats	Pancreas	Pancrea
5	chr6:25758000-25758600	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr6:25758400-25758600	Active TSS	Duodenum Mucosa	Duodenum
7	chr6:25758400-25758600	Flanking Active TSS	Fetal Intestine Small	intestine
8	chr6:25758400-25758600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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