Variant report

Variant	rs6673009
Chromosome Location	chr1:171901805-171901806
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10737340	0.85[CEU][hapmap]
rs10914141	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap]
rs12120554	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12121064	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12122025	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12123334	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12123946	1.00[ASN][1000 genomes]
rs12125022	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12130277	1.00[ASN][1000 genomes]
rs12133814	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12134649	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12135871	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136630	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12137824	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137825	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140482	0.86[ASN][1000 genomes]
rs12140603	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12141726	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141865	0.86[ASN][1000 genomes]
rs12143501	0.86[ASN][1000 genomes]
rs12144607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12145177	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17472925	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs2421949	1.00[ASN][1000 genomes]
rs3817923	0.86[ASN][1000 genomes]
rs61805807	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61805811	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61805813	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61805815	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61805816	0.83[EUR][1000 genomes]
rs74126507	0.86[ASN][1000 genomes]
rs74126515	0.86[ASN][1000 genomes]
rs74126524	0.86[ASN][1000 genomes]
rs74126528	1.00[ASN][1000 genomes]
rs7543247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6673009	ILDR2	cis	parietal	SCAN
rs6673009	FMO9P	cis	cerebellum	SCAN
rs6673009	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL
rs6673009	BRP44	cis	parietal	SCAN
rs6673009	CUTC	trans	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171879800-171908000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:171884200-171903400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:171886800-171902800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:171889800-171902600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:171897800-171902600	Weak transcription	Gastric	stomach
6	chr1:171899000-171902000	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:171899800-171902200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:171899800-171905200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:171900000-171916200	Weak transcription	Lung	lung
10	chr1:171900200-171905800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:171900400-171903600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:171901800-171904000	Enhancers	Brain Substantia Nigra	brain

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