Variant report

Variant	rs17652674
Chromosome Location	chr15:38900312-38900313
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:38893098..38895814-chr15:38898474..38901453,3	MCF-7	breast:
2	chr15:38899048..38900871-chr15:38903467..38905041,2	K562	blood:
3	chr15:38884414..38892257-chr15:38898196..38905033,11	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10520096	0.90[AFR][1000 genomes]
rs16967103	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16967104	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16967112	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16967120	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs17574546	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17651741	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17653133	0.84[EUR][1000 genomes]
rs28438860	0.83[CEU][hapmap]
rs4614699	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55762999	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55791667	0.84[EUR][1000 genomes]
rs56059718	0.81[EUR][1000 genomes]
rs56083426	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56165729	0.83[EUR][1000 genomes]
rs56249992	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56279249	0.86[EUR][1000 genomes]
rs60455438	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60924694	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61109886	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61573680	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7171171	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72729306	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72729314	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72729320	0.85[EUR][1000 genomes]
rs72729321	0.83[EUR][1000 genomes]
rs72729322	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949171	chr15:38232548-39033746	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv904085	chr15:38786114-38985513	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1046994	chr15:38806163-39239014	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv525770	chr15:38816833-39084956	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1054651	chr15:38827825-39082844	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv542358	chr15:38827825-39082844	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv904086	chr15:38829198-38931396	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17652674	RASGRP1	Cis_1M	lymphoblastoid	RTeQTL
rs17652674	RP11-275I4.2	cis	Esophagus Mucosa	GTEx
rs17652674	RASGRP1	cis	Skin Sun Exposed Lower leg	GTEx
rs17652674	RP11-102L12.2	cis	Esophagus Mucosa	GTEx
rs17652674	RASGRP1	cis	Esophagus Mucosa	GTEx
rs17652674	RASGRP1	cis	normal skin	skin_eQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38886800-38902600	Weak transcription	Primary T cells from cord blood	blood
2	chr15:38891000-38902600	Weak transcription	Thymus	Thymus
3	chr15:38894400-38901400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:38896400-38901600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr15:38896400-38903400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:38898600-38901800	Weak transcription	Placenta	Placenta
7	chr15:38898600-38903000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:38899200-38900600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:38899800-38903000	Weak transcription	K562	blood

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