Variant report

Variant	rs2412748
Chromosome Location	chr15:43227515-43227516
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10518779	0.95[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs16957168	0.94[ASW][hapmap];0.90[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs16957422	0.94[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap]
rs28374998	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28494835	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28609797	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28613047	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28620320	0.81[EUR][1000 genomes]
rs28633493	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28796057	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28810091	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28871732	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3759792	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4274403	0.83[AMR][1000 genomes]
rs4924699	0.80[CEU][hapmap]
rs4924705	0.88[ASW][hapmap];0.95[CEU][hapmap];0.80[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap]
rs66947001	0.88[EUR][1000 genomes]
rs7166705	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7166775	0.81[CEU][hapmap];0.94[JPT][hapmap]
rs7167392	0.85[MEX][hapmap]
rs7169009	0.94[JPT][hapmap]
rs7170376	0.83[AMR][1000 genomes]
rs7175582	0.95[CEU][hapmap]
rs7176957	0.94[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];0.87[AMR][1000 genomes]
rs7178248	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7181859	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7182141	0.94[ASW][hapmap];0.90[CEU][hapmap]
rs7182650	0.83[AMR][1000 genomes]
rs8028785	0.88[ASW][hapmap];0.95[CEU][hapmap];0.87[GIH][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs8036674	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8037613	0.80[CEU][hapmap]
rs9920061	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9920182	1.00[ASW][hapmap];0.95[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9920202	0.95[CEU][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050128	chr15:43056145-43262736	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv542368	chr15:43056145-43262736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv904134	chr15:43097652-43357406	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv904135	chr15:43143998-43392075	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1036512	chr15:43164906-43274531	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv569239	chr15:43201109-43392075	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv569240	chr15:43201109-43445305	Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv1039587	chr15:43204351-43378274	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv569242	chr15:43210030-43445305	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv974565	chr15:43225638-43234039	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2412748	CDAN1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43222400-43236600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr15:43223600-43238400	Weak transcription	Ovary	ovary
3	chr15:43225800-43236000	Weak transcription	HUVEC	blood vessel
4	chr15:43225800-43247600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr15:43226000-43242200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:43226400-43227600	Weak transcription	HMEC	breast
7	chr15:43226400-43228200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:43226400-43228200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:43226400-43235400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:43226600-43235400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr15:43226800-43233000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:43227000-43228200	Enhancers	NHEK	skin
13	chr15:43227400-43228000	Enhancers	HepG2	liver
14	chr15:43227400-43228600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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