Variant report

Variant	rs56279249
Chromosome Location	chr15:38915313-38915314
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:38900766..38902547-chr15:38915124..38917930,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs16967103	0.85[EUR][1000 genomes]
rs16967104	0.86[EUR][1000 genomes]
rs16967112	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16967120	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17574546	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17652674	0.86[EUR][1000 genomes]
rs17653133	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4614699	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55762999	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55791667	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56083426	0.83[EUR][1000 genomes]
rs56165729	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56249992	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60455438	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60924694	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61109886	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61573680	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7164418	0.82[EUR][1000 genomes]
rs7171171	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7173588	0.82[EUR][1000 genomes]
rs72729306	0.85[EUR][1000 genomes]
rs72729314	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72729320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72729321	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72729322	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56279249	RASGRP1	Cis_1M	lymphoblastoid	RTeQTL
rs56279249	RASGRP1	cis	Skin Sun Exposed Lower leg	GTEx
rs56279249	RASGRP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38910800-38918000	Weak transcription	Left Ventricle	heart
2	chr15:38912200-38916000	Enhancers	Fetal Thymus	thymus
3	chr15:38912400-38916000	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr15:38912800-38917200	Enhancers	Fetal Intestine Large	intestine
5	chr15:38913400-38915800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr15:38913400-38918200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr15:38913400-38918400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:38913400-38918400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr15:38913400-38918600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:38913600-38916000	Weak transcription	Fetal Stomach	stomach
11	chr15:38913600-38918000	Weak transcription	Fetal Heart	heart
12	chr15:38913600-38918000	Weak transcription	Dnd41	blood
13	chr15:38913600-38918200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:38913600-38918200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:38913600-38918200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr15:38913600-38918400	Weak transcription	Primary T cells from cord blood	blood
17	chr15:38913600-38918400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr15:38913800-38918200	Weak transcription	Thymus	Thymus
19	chr15:38913800-38918400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr15:38913800-38918400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr15:38913800-38918600	Weak transcription	Fetal Kidney	kidney
22	chr15:38913800-38919200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr15:38914200-38915600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:38914200-38918000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:38914400-38918000	Weak transcription	Fetal Brain Male	brain
26	chr15:38914600-38915400	Enhancers	Pancreas	Pancrea
27	chr15:38914600-38917000	Enhancers	Fetal Intestine Small	intestine
28	chr15:38914600-38918400	Weak transcription	Fetal Brain Female	brain
29	chr15:38914800-38916800	Enhancers	Placenta	Placenta
30	chr15:38914800-38922000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:38915000-38916200	Enhancers	Primary T cells fromperipheralblood	blood
32	chr15:38915200-38915400	Enhancers	Lung	lung
33	chr15:38915200-38915400	Enhancers	Psoas Muscle	Psoas
34	chr15:38915200-38916000	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr15:38915200-38916400	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr15:38915200-38916800	Enhancers	Stomach Mucosa	stomach

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