Variant report

Variant	rs12077603
Chromosome Location	chr1:171961138-171961139
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10158884	0.84[AMR][1000 genomes]
rs1073940	0.94[CEU][hapmap];0.94[MEX][hapmap];0.80[AMR][1000 genomes]
rs10910863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10910881	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10910891	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12073819	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088862	0.82[AMR][1000 genomes]
rs12403863	0.94[CEU][hapmap];0.88[MEX][hapmap]
rs12408359	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843679	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843681	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2208370	0.81[CHB][hapmap];0.91[CHD][hapmap];0.86[ASN][1000 genomes]
rs2208371	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2224396	0.81[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs2421950	0.87[CEU][hapmap];0.83[MEX][hapmap]
rs3736790	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55682753	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6667114	0.94[CEU][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs6668677	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680084	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684633	0.84[AMR][1000 genomes]
rs6702539	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525638	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546327	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3399662	chr1:171961064-171961295	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12077603	ANKRD45	cis	parietal	SCAN
rs12077603	CD247	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171949000-171976000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:171949400-171963600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:171952800-171962000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:171953800-171964800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:171953800-171967800	Weak transcription	Left Ventricle	heart
6	chr1:171954400-171968000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:171956000-171961200	Weak transcription	Adipose Nuclei	Adipose
8	chr1:171958800-171966800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:171959400-171963400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:171959600-171966600	Weak transcription	Brain Anterior Caudate	brain
11	chr1:171959800-171968000	Weak transcription	Brain Angular Gyrus	brain
12	chr1:171960000-171969400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:171960200-171964400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:171960200-171964400	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:171960200-171966400	Weak transcription	Brain Substantia Nigra	brain

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