Variant report

Variant	rs72727387
Chromosome Location	chr15:38843476-38843477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:38843328..38846327-chr15:38850972..38852762,3	MCF-7	breast:
2	chr15:38841371..38843704-chr15:38854778..38857047,2	MCF-7	breast:
3	chr15:38841980..38844284-chr15:38845955..38848635,3	MCF-7	breast:
4	chr15:38838012..38840688-chr15:38841351..38843546,2	MCF-7	breast:
5	chr15:38842649..38844707-chr15:38853512..38856780,3	MCF-7	breast:
6	chr15:38841426..38843613-chr15:38851197..38853215,2	MCF-7	breast:
7	chr15:38837304..38840983-chr15:38841672..38845107,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172575	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11073333	0.80[AMR][1000 genomes]
rs11073334	0.80[AMR][1000 genomes]
rs11073337	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11631591	0.87[EUR][1000 genomes]
rs12593201	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28582094	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924273	0.89[EUR][1000 genomes]
rs6495979	0.90[EUR][1000 genomes]
rs7170151	0.89[EUR][1000 genomes]
rs7173565	0.87[EUR][1000 genomes]
rs72727388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7403531	0.80[AMR][1000 genomes]
rs8032939	0.81[EUR][1000 genomes]
rs8035957	0.86[EUR][1000 genomes]
rs8043085	0.83[AMR][1000 genomes];0.86[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72727387	RASGRP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38812600-38845400	Weak transcription	Fetal Brain Female	brain
2	chr15:38827400-38853800	Weak transcription	Esophagus	oesophagus
3	chr15:38828000-38851000	Weak transcription	Spleen	Spleen
4	chr15:38831600-38845200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:38833800-38845600	Weak transcription	Fetal Intestine Large	intestine
6	chr15:38836200-38855800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:38838600-38850400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:38839600-38843600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr15:38839600-38848800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr15:38839800-38844000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:38839800-38844200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:38840000-38844400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:38841400-38845200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:38841400-38849200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr15:38841600-38854400	Weak transcription	Dnd41	blood
16	chr15:38842000-38844200	Weak transcription	Primary B cells from cord blood	blood
17	chr15:38842000-38845000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:38842000-38845000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:38842000-38845800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr15:38842000-38846200	Weak transcription	GM12878-XiMat	blood
21	chr15:38842200-38844200	Enhancers	Primary T cells from cord blood	blood
22	chr15:38842200-38844200	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr15:38842200-38845200	Weak transcription	Thymus	Thymus
24	chr15:38842200-38845600	Weak transcription	HSMM	muscle
25	chr15:38842200-38846200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:38842400-38845200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:38843000-38846000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:38843400-38843600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr15:38843400-38844400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:38843400-38844600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr15:38843400-38844600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:38843400-38844800	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr15:38843400-38845200	Strong transcription	Fetal Thymus	thymus
34	chr15:38843400-38845600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:38843400-38845600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr15:38843400-38848200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
37	chr15:38843400-38849800	Genic enhancers	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links