Variant report

Variant	rs12024396
Chromosome Location	chr1:97880883-97880884
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10875077	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10875078	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10875079	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165862	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12143861	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12409761	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1879371	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4319378	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4589145	0.83[ASN][1000 genomes]
rs4634942	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6672867	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6699630	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7515904	0.94[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7521383	0.84[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7536690	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs955850	0.94[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][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	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv871806	chr1:97855607-97885200	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12024396	CCDC76	cis	cerebellum	SCAN
rs12024396	GPR88	cis	parietal	SCAN
rs12024396	SASS6	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97846600-97886800	Weak transcription	Dnd41	blood
2	chr1:97847200-97912600	Weak transcription	Primary B cells from cord blood	blood
3	chr1:97861600-97888600	Weak transcription	Left Ventricle	heart
4	chr1:97861600-97930000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:97868800-97913000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr1:97869400-97887800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:97872600-98014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:97872800-97912200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:97873000-97885600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:97874400-97888800	Weak transcription	Brain Anterior Caudate	brain
11	chr1:97875600-97881600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr1:97875600-97888400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:97877000-97904800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr1:97878000-97882000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:97878200-97882000	Weak transcription	Adipose Nuclei	Adipose
16	chr1:97878600-97888400	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:97878800-97885600	Weak transcription	Primary T cells from cord blood	blood
18	chr1:97878800-97888200	Weak transcription	Brain Angular Gyrus	brain
19	chr1:97878800-97898400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:97879000-97882000	Weak transcription	Brain Substantia Nigra	brain
21	chr1:97879600-97894800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:97880600-97881600	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links