Variant report

Variant	rs56059718
Chromosome Location	chr15:38836777-38836778
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:38836755..38838445-chr15:38851683..38853493,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172575	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16967103	0.82[EUR][1000 genomes]
rs16967104	0.81[EUR][1000 genomes]
rs17651741	0.87[EUR][1000 genomes]
rs17652674	0.81[EUR][1000 genomes]
rs56083426	0.83[EUR][1000 genomes]
rs60924694	0.80[EUR][1000 genomes]
rs61109886	0.80[EUR][1000 genomes]
rs61573680	0.80[EUR][1000 genomes]
rs7171171	0.80[EUR][1000 genomes]
rs7178883	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72727394	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72729306	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56059718	RASGRP1	Cis_1M	lymphoblastoid	RTeQTL
rs56059718	RASGRP1	cis	Skin Sun Exposed Lower leg	GTEx
rs56059718	RASGRP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38804000-38841000	Weak transcription	Dnd41	blood
2	chr15:38812600-38845400	Weak transcription	Fetal Brain Female	brain
3	chr15:38825600-38838800	Weak transcription	GM12878-XiMat	blood
4	chr15:38827400-38853800	Weak transcription	Esophagus	oesophagus
5	chr15:38828000-38851000	Weak transcription	Spleen	Spleen
6	chr15:38829600-38841200	Weak transcription	NHDF-Ad	bronchial
7	chr15:38830800-38837000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:38831200-38838000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr15:38831400-38838000	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr15:38831600-38838000	Strong transcription	Fetal Thymus	thymus
11	chr15:38831600-38838800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr15:38831600-38845200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:38832400-38838200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
14	chr15:38832800-38837000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:38833000-38838600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr15:38833800-38845600	Weak transcription	Fetal Intestine Large	intestine
17	chr15:38834400-38839000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:38834400-38839000	Weak transcription	Thymus	Thymus
19	chr15:38834400-38840600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:38834800-38838800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr15:38834800-38839000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr15:38835400-38836800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:38836200-38837200	Genic enhancers	Primary T cells from cord blood	blood
24	chr15:38836200-38838000	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr15:38836200-38839800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:38836200-38843400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr15:38836200-38855800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:38836400-38837000	Weak transcription	Primary B cells from cord blood	blood
29	chr15:38836400-38837000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
30	chr15:38836600-38836800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:38836600-38836800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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