Variant report

Variant	rs56249992
Chromosome Location	chr15:38903884-38903885
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:38902462..38904762-chr15:38908656..38911078,2	MCF-7	breast:
2	chr15:38884414..38892257-chr15:38898196..38905033,11	MCF-7	breast:
3	chr15:38899048..38900871-chr15:38903467..38905041,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs16967103	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16967104	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16967112	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16967120	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17574546	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17651741	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17652674	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17653133	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4614699	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55762999	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55791667	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56083426	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56165729	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56279249	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60455438	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60924694	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61109886	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61573680	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171171	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72729306	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72729314	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72729320	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72729321	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72729322	0.85[EUR][1000 genomes];0.83[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs56249992	RASGRP1	cis	Skin Sun Exposed Lower leg	GTEx
rs56249992	RASGRP1	cis	Esophagus Mucosa	GTEx
rs56249992	RP11-102L12.2	cis	Esophagus Mucosa	GTEx
rs56249992	RASGRP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38901200-38905600	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr15:38901200-38905800	Enhancers	Primary T cells fromperipheralblood	blood
3	chr15:38901200-38905800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr15:38901200-38905800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr15:38901200-38906000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:38901200-38913400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:38901600-38904600	Enhancers	Primary B cells from peripheral blood	blood
8	chr15:38902200-38906000	Enhancers	Fetal Thymus	thymus
9	chr15:38902400-38904200	Enhancers	Primary B cells from cord blood	blood
10	chr15:38902600-38905000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:38902600-38905800	Enhancers	Thymus	Thymus
12	chr15:38902800-38905400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr15:38903000-38904000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr15:38903000-38905600	Enhancers	Dnd41	blood
15	chr15:38903200-38904200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr15:38903400-38904000	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr15:38903400-38904200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:38903600-38905600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:38903800-38904200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:38903800-38904200	Enhancers	Primary T helper cells PMA-I stimulated	--

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