Variant report

Variant	rs999197
Chromosome Location	chr15:40795198-40795199
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	chr15:40788119..40791373-chr15:40792541..40795559,4	K562	blood:
2	chr15:40731663..40736686-chr15:40795056..40800792,8	K562	blood:

Variant related genes	Relation type
ENSG00000140320	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10152546	0.87[YRI][hapmap]
rs1044474	0.91[YRI][hapmap]
rs1051482	0.96[CEU][hapmap]
rs1058734	0.83[YRI][hapmap]
rs10851396	0.92[CEU][hapmap]
rs11070279	0.92[CEU][hapmap]
rs11852527	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11857247	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12148185	0.96[CEU][hapmap]
rs12907448	0.95[CEU][hapmap]
rs12908114	0.92[CEU][hapmap]
rs12915563	0.88[CEU][hapmap]
rs12916323	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1453183	0.96[CEU][hapmap]
rs16970758	0.81[YRI][hapmap]
rs17673703	0.91[YRI][hapmap]
rs1901774	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2053973	0.95[YRI][hapmap]
rs2123534	0.86[EUR][1000 genomes]
rs2412524	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2412545	0.87[CEU][hapmap]
rs3213999	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35030447	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36122190	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4457966	0.96[CEU][hapmap]
rs5030783	0.88[CEU][hapmap]
rs61048252	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62018030	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62018046	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62018048	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62018051	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7164385	0.87[EUR][1000 genomes]
rs7181909	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72733469	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs731640	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs733299	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs8025458	0.96[CEU][hapmap]
rs8028910	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9672313	0.80[CEU][hapmap]
rs9806410	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs999197	C15orf57	cis	Adipose Subcutaneous	GTEx
rs999197	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs999197	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs999197	C15orf57	cis	Esophagus Muscularis	GTEx
rs999197	CCDC32	cis	lesional skin	skin_eQTL
rs999197	C15orf57	cis	Artery Tibial	GTEx
rs999197	C15orf57	cis	Lymphoblastoid	GTEx
rs999197	RP11-111A22.1	cis	Artery Tibial	GTEx
rs999197	MGC20481	cis	multi-tissue	Pritchard
rs999197	C15orf57	cis	lung	GTEx
rs999197	C15orf57	cis	Cerebellum	GTEx
rs999197	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs999197	CCDC32	cis	multi-tissue	Pritchard
rs999197	CCDC32	cis	normal skin	skin_eQTL
rs999197	RP11-111A22.1	cis	lung	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40786600-40799200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:40793400-40797200	Weak transcription	K562	blood
3	chr15:40793600-40798800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:40793800-40799200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:40793800-40799200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:40793800-40799200	Weak transcription	HMEC	breast
7	chr15:40794000-40798800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:40794000-40799000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:40794000-40799000	Weak transcription	NHEK	skin
10	chr15:40794000-40799200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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