Variant report

Variant	rs28438860
Chromosome Location	chr15:38858062-38858063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17651741	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72727394	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	esv3415080	chr15:38855685-38858233	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28438860	RASGRP1	Cis_1M	lymphoblastoid	RTeQTL
rs28438860	RP11-102L12.2	cis	Esophagus Mucosa	GTEx
rs28438860	C15orf41	cis	cerebellum	SCAN
rs28438860	ARHGAP11A	cis	parietal	SCAN
rs28438860	RASGRP1	cis	Skin Sun Exposed Lower leg	GTEx
rs28438860	RASGRP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38857200-38858400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr15:38857600-38859200	Enhancers	Fetal Thymus	thymus
3	chr15:38857600-38859400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:38857800-38858200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
5	chr15:38857800-38858400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr15:38857800-38859000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:38857800-38859200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:38857800-38859200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr15:38857800-38859200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:38857800-38859400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr15:38857800-38859600	Enhancers	Primary T cells from cord blood	blood
12	chr15:38857800-38859600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr15:38857800-38859800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr15:38858000-38859000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:38858000-38859000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr15:38858000-38859200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr15:38858000-38859400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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