Variant report

Variant	rs12440708
Chromosome Location	chr15:30129321-30129322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:30115117..30117286-chr15:30127029..30129725,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10152681	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10775231	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11073205	0.86[EUR][1000 genomes]
rs11073218	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11636849	0.83[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]
rs12438925	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs12440211	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12441554	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1383315	0.93[ASW][hapmap];0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1480503	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1552077	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap]
rs1585900	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2032	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2229518	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2337167	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs260531	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs260532	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs260533	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs260534	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs260535	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs28675809	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2878893	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2878905	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4073316	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs4362339	0.94[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs4779670	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4780259	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4780260	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4780263	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6495890	0.84[EUR][1000 genomes]
rs6495914	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6495927	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6495935	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6495945	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7166786	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7168919	0.93[ASW][hapmap];0.94[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7170406	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs7171815	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7175819	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7176476	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7176594	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs7180387	0.87[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs767514	0.93[ASW][hapmap];0.88[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs785445	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs785446	0.82[CEU][hapmap]
rs8023974	0.82[EUR][1000 genomes]
rs8027827	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv903754	chr15:30023454-30382120	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv903755	chr15:30036085-30351434	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv1851951	chr15:30043659-30178871	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv1845759	chr15:30097078-30142373	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv482572	chr15:30118905-30304529	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12440708	C15orf2	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30115600-30132800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr15:30115600-30136000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:30120200-30132600	Weak transcription	Right Ventricle	heart
4	chr15:30121800-30132600	Weak transcription	Right Atrium	heart
5	chr15:30125200-30132600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:30125200-30135800	Weak transcription	Spleen	Spleen
7	chr15:30127400-30133200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:30127800-30131600	Weak transcription	Liver	Liver
9	chr15:30127800-30132200	Weak transcription	Brain Hippocampus Middle	brain
10	chr15:30127800-30132800	Weak transcription	Brain Anterior Caudate	brain
11	chr15:30127800-30136000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:30128000-30130000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:30128000-30130000	Weak transcription	HSMMtube	muscle
14	chr15:30128000-30132000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:30128000-30133000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:30128000-30136000	Weak transcription	Lung	lung
17	chr15:30128200-30133000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:30128200-30133000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:30128400-30129800	Weak transcription	Fetal Heart	heart
20	chr15:30128400-30130000	Weak transcription	HSMM	muscle
21	chr15:30128400-30130400	Weak transcription	NHEK	skin
22	chr15:30128400-30130600	Weak transcription	HMEC	breast
23	chr15:30128400-30132800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:30128400-30132800	Weak transcription	Brain Angular Gyrus	brain
25	chr15:30128400-30133000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr15:30128400-30136000	Weak transcription	Esophagus	oesophagus
27	chr15:30128600-30129800	Enhancers	Left Ventricle	heart
28	chr15:30128600-30130600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:30129000-30132200	Weak transcription	Brain Substantia Nigra	brain
30	chr15:30129200-30132600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links