Variant report

Variant	rs12040542
Chromosome Location	chr1:9591499-9591500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9589297..9593033-chr1:9598023..9601715,4	K562	blood:
2	chr1:9589698..9594736-chr1:9596455..9600782,9	K562	blood:
3	chr1:9588957..9591794-chr1:9592247..9595158,3	K562	blood:

Variant related genes	Relation type
ENSG00000171612	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10864429	0.86[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12022881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023288	0.81[CEU][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.85[ASN][1000 genomes]
rs12037667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045459	0.85[ASN][1000 genomes]
rs12045493	0.85[ASN][1000 genomes]
rs12070568	0.86[ASN][1000 genomes]
rs12084279	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3923984	0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.86[ASN][1000 genomes]
rs4073710	0.89[JPT][hapmap];0.96[TSI][hapmap]
rs4074744	0.94[ASW][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs4423053	0.81[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap]
rs55655211	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55687246	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55780537	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55986711	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56012411	0.85[EUR][1000 genomes]
rs57272167	0.87[ASN][1000 genomes]
rs58478478	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60744607	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540961	0.94[ASW][hapmap];0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs6540962	0.94[ASW][hapmap];0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs6698575	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.90[ASN][1000 genomes]
rs72646706	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72646708	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72646709	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72646711	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72646712	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72646713	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72646715	0.92[ASN][1000 genomes]
rs72646718	0.80[ASN][1000 genomes]
rs7411273	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.98[ASN][1000 genomes]
rs7525099	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7544083	0.81[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap]
rs9430152	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs9430153	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs9430174	0.94[ASW][hapmap];0.81[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.86[ASN][1000 genomes]
rs9430182	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs9430184	0.95[JPT][hapmap]
rs9430273	0.94[ASW][hapmap];0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9430274	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9430332	0.81[CEU][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap]

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	nsv931984	chr1:8879337-9694749	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	570 gene(s)	inside rSNPs	diseases
2	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
3	nsv1013224	chr1:9441040-9699768	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv464283	chr1:9495571-9677853	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv545363	chr1:9495571-9677853	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12040542	NPPA	cis	cerebellum	SCAN
rs12040542	SDC1	trans	lymphoblastoid	seeQTL
rs12040542	HNRNPCL1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9555800-9599400	Weak transcription	Right Atrium	heart
2	chr1:9585200-9592600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:9587200-9598200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:9589400-9592000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:9589600-9592200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:9589800-9592000	Enhancers	HepG2	liver
7	chr1:9589800-9592800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:9590000-9592600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:9590000-9592800	Weak transcription	Brain Anterior Caudate	brain
10	chr1:9590000-9593000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:9590400-9592200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:9590400-9592200	Weak transcription	Brain Angular Gyrus	brain
13	chr1:9590400-9593200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:9590600-9592800	Weak transcription	Brain Substantia Nigra	brain
15	chr1:9590600-9593200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:9591200-9591600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:9591200-9591600	Enhancers	Rectal Smooth Muscle	rectum
18	chr1:9591200-9591600	Enhancers	HMEC	breast
19	chr1:9591200-9592000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:9591200-9592000	Enhancers	Fetal Heart	heart
21	chr1:9591400-9591600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:9591400-9591600	Enhancers	Adipose Nuclei	Adipose
23	chr1:9591400-9592800	Weak transcription	Liver	Liver

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