Variant report

Variant	rs61805845
Chromosome Location	chr1:171952008-171952009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10914141	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120554	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12122025	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12123334	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12125022	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12135615	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137105	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144607	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12145177	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17472925	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61805811	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61805813	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61805815	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61805816	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6684723	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691703	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv831893	chr1:171802450-171985000	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61805845	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171937400-171958000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:171941800-171954600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:171949000-171976000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:171949200-171953000	Weak transcription	Brain Anterior Caudate	brain
5	chr1:171949200-171953600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:171949400-171953200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:171949400-171963600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:171949800-171953000	Weak transcription	Brain Substantia Nigra	brain
9	chr1:171950200-171953400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:171950200-171955400	Enhancers	Brain Hippocampus Middle	brain
11	chr1:171950400-171953200	Weak transcription	Brain Angular Gyrus	brain
12	chr1:171950600-171953000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:171951000-171957000	Weak transcription	Fetal Brain Male	brain
14	chr1:171951600-171952800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:171952000-171952800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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

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