Variant report

Variant	rs6703170
Chromosome Location	chr1:226975270-226975271
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12132893	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409752	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12738352	1.00[YRI][hapmap]
rs1800681	0.93[JPT][hapmap]
rs3213436	0.91[CHD][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap]
rs6426554	0.81[JPT][hapmap]
rs6676067	0.93[JPT][hapmap]
rs708761	0.86[CEU][hapmap]
rs732479	0.93[JPT][hapmap]

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	nsv997468	chr1:226858660-226975311	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv535316	chr1:226858660-226975311	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6703170	PSEN2	cis	parietal	SCAN
rs6703170	PSEN2	cis	cerebellum	SCAN
rs6703170	CNIH3	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226966600-226986400	Weak transcription	Right Atrium	heart
2	chr1:226969600-226976400	Enhancers	Brain Cingulate Gyrus	brain
3	chr1:226970800-226977000	Enhancers	Rectal Smooth Muscle	rectum
4	chr1:226971000-226976400	Enhancers	Colon Smooth Muscle	Colon
5	chr1:226971200-226976400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:226971600-226986800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:226972000-226975600	Enhancers	Brain Anterior Caudate	brain
8	chr1:226972200-226976600	Enhancers	Stomach Smooth Muscle	stomach
9	chr1:226973200-226976200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:226973600-226976000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:226974200-226976400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:226974200-226976400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:226974400-226976200	Enhancers	Fetal Stomach	stomach
14	chr1:226974400-226976400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:226974800-226976000	Weak transcription	Brain Angular Gyrus	brain
16	chr1:226975000-226975600	Active TSS	Brain Substantia Nigra	brain
17	chr1:226975000-226976200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:226975200-226975400	Enhancers	Brain Hippocampus Middle	brain
19	chr1:226975200-226976600	Enhancers	GM12878-XiMat	blood

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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