Variant report

Variant	rs3798995
Chromosome Location	chr6:69700760-69700761
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12665384	0.82[ASW][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12665411	0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1336654	0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1415032	0.90[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1572940	0.84[EUR][1000 genomes]
rs1953614	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757049	0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs3798971	0.83[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3798982	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798983	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798990	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798997	0.82[ASW][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3799019	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs72906776	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9360369	1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs960991	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9718113	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv5338	chr6:69670701-69701360	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv886137	chr6:69684850-70095690	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3798995	AHNAK2	trans	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69685800-69758800	Weak transcription	Fetal Brain Male	brain
2	chr6:69686200-69703400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr6:69686800-69706200	Weak transcription	Fetal Lung	lung
4	chr6:69688200-69721200	Weak transcription	Left Ventricle	heart
5	chr6:69692000-69716600	Weak transcription	Fetal Stomach	stomach
6	chr6:69695200-69704400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:69696200-69703400	Weak transcription	Fetal Brain Female	brain
8	chr6:69696400-69715400	Weak transcription	Aorta	Aorta
9	chr6:69700000-69701000	Enhancers	Brain Hippocampus Middle	brain
10	chr6:69700000-69702400	Enhancers	Brain Angular Gyrus	brain
11	chr6:69700200-69701000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:69700200-69701000	Enhancers	Brain Substantia Nigra	brain
13	chr6:69700200-69701200	Enhancers	Brain Cingulate Gyrus	brain
14	chr6:69700400-69700800	Enhancers	Brain Anterior Caudate	brain
15	chr6:69700400-69701000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:69700400-69701200	Enhancers	Brain Germinal Matrix	brain
17	chr6:69700600-69701200	Enhancers	Brain Inferior Temporal Lobe	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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