Variant report

Variant	rs8023437
Chromosome Location	chr15:45827343-45827344
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45821890..45824592-chr15:45826974..45829188,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179362	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10152697	0.86[CHB][hapmap]
rs10851425	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1153829	0.88[ASW][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap]
rs1153830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1153831	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1153832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1288861	0.88[CHB][hapmap]
rs1288863	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1288865	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1529354	0.84[LWK][hapmap]
rs16944305	0.84[LWK][hapmap]
rs16944629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16952731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs17535381	0.88[CHB][hapmap]
rs17537244	0.93[CEU][hapmap];0.88[CHB][hapmap];0.81[TSI][hapmap]
rs1768458	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2088164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2433600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2433617	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2433619	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2486287	0.88[CHB][hapmap]
rs35828336	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4448883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55997350	0.85[EUR][1000 genomes]
rs56179992	0.94[EUR][1000 genomes]
rs56405528	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59574269	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60350201	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60992352	0.94[EUR][1000 genomes]
rs61193305	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493154	0.94[ASW][hapmap];0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493157	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493160	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7165838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7166434	0.95[LWK][hapmap];0.83[YRI][hapmap]
rs7169748	1.00[CEU][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7170090	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs7171406	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7173983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72711264	0.85[ASN][1000 genomes]
rs72711278	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72711279	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72711280	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72711283	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72711284	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72711290	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72711294	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72711301	0.94[EUR][1000 genomes]
rs72713103	0.94[EUR][1000 genomes]
rs72713104	0.92[EUR][1000 genomes]
rs72713105	0.92[EUR][1000 genomes]
rs8025407	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes]
rs8029509	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8040466	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8042811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9972498	0.88[CHB][hapmap]

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	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1045556	chr15:45777396-45884854	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv904188	chr15:45801035-45941689	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8023437	RPAP1	cis	cerebellum	SCAN
rs8023437	FAM82A2	cis	cerebellum	SCAN
rs8023437	MGA	cis	parietal	SCAN
rs8023437	SLC30A4	cis	parietal	SCAN
rs8023437	GPR176	cis	cerebellum	SCAN
rs8023437	TMEM62	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45825600-45827800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:45826400-45828400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:45826600-45828400	Enhancers	Brain Anterior Caudate	brain
4	chr15:45826600-45828600	Enhancers	Brain Hippocampus Middle	brain
5	chr15:45826600-45828600	Enhancers	Brain Substantia Nigra	brain
6	chr15:45826800-45827800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:45826800-45827800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr15:45826800-45828200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr15:45826800-45828200	Enhancers	Brain Angular Gyrus	brain
10	chr15:45826800-45828600	Enhancers	Brain Cingulate Gyrus	brain
11	chr15:45827000-45827600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:45827200-45827600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:45827200-45828000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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