Variant report

Variant	rs56165729
Chromosome Location	chr15:38920179-38920180
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	chr15:38856173..38856790-chr15:38919910..38920706,2	MCF-7	breast:
2	chr15:38855034..38857196-chr15:38918448..38921034,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172575	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs16967103	0.83[EUR][1000 genomes]
rs16967104	0.83[EUR][1000 genomes]
rs16967112	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16967120	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17574546	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17652674	0.83[EUR][1000 genomes]
rs17653133	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4614699	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55762999	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55791667	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56083426	0.81[EUR][1000 genomes]
rs56249992	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56279249	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59659806	0.85[EUR][1000 genomes]
rs60455438	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60924694	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61109886	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61573680	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7171171	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72729306	0.83[EUR][1000 genomes]
rs72729314	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72729320	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72729321	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72729322	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883625	0.86[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56165729	RASGRP1	cis	Esophagus Mucosa	GTEx
rs56165729	RASGRP1	cis	Skin Sun Exposed Lower leg	GTEx
rs56165729	RASGRP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38914800-38922000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:38916400-38923000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:38916800-38922800	Weak transcription	GM12878-XiMat	blood
4	chr15:38918000-38920400	Enhancers	Fetal Brain Male	brain
5	chr15:38918000-38920600	Enhancers	Fetal Heart	heart
6	chr15:38918200-38920200	Enhancers	Fetal Thymus	thymus
7	chr15:38918200-38920600	Enhancers	Fetal Intestine Small	intestine
8	chr15:38918800-38923200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:38919200-38922800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:38919200-38923400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr15:38919400-38921800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr15:38919400-38922000	Weak transcription	Thymus	Thymus
13	chr15:38919400-38922800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr15:38919400-38923200	Weak transcription	Primary T cells from cord blood	blood
15	chr15:38919400-38923200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:38919400-38923200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr15:38919400-38923400	Weak transcription	Dnd41	blood
18	chr15:38919400-38923600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr15:38919400-38923600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr15:38919400-38923800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr15:38919600-38923400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:38919800-38920800	Enhancers	Duodenum Mucosa	Duodenum
23	chr15:38919800-38921000	Enhancers	Fetal Intestine Large	intestine
24	chr15:38920000-38920200	Enhancers	Fetal Brain Female	brain
25	chr15:38920000-38920600	Flanking Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links