Variant report

Variant	rs4924273
Chromosome Location	chr15:38846738-38846739
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:38846655..38849708-chr15:38855681..38858182,3	K562	blood:
2	chr10:70092013..70094325-chr15:38846600..38849619,3	K562	blood:
3	chr15:38846255..38849708-chr15:38855681..38858197,3	K562	blood:
4	chr15:38838794..38843031-chr15:38844635..38848168,4	MCF-7	breast:
5	chr15:38841980..38844284-chr15:38845955..38848635,3	MCF-7	breast:
6	chr15:38839756..38843120-chr15:38845025..38847998,3	K562	blood:
7	chr15:38843675..38845266-chr15:38845646..38848503,2	K562	blood:

Variant related genes	Relation type
ENSG00000108187	Chromatin interaction
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]
rs11073337	1.00[CEU][hapmap];0.81[TSI][hapmap];0.93[EUR][1000 genomes]
rs11631591	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12593201	1.00[CEU][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs28582094	0.89[EUR][1000 genomes]
rs6495979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7170151	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173565	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72727387	0.89[EUR][1000 genomes]
rs72727388	0.89[EUR][1000 genomes]
rs8032939	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8035957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8043085	0.92[CEU][hapmap];0.80[MEX][hapmap]

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
rs4924273	RASGRP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4924273	RASGRP1	Cis_1M	lymphoblastoid	RTeQTL
rs4924273	RASGRP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38827400-38853800	Weak transcription	Esophagus	oesophagus
2	chr15:38828000-38851000	Weak transcription	Spleen	Spleen
3	chr15:38836200-38855800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:38838600-38850400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:38839600-38848800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
6	chr15:38841400-38849200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr15:38841600-38854400	Weak transcription	Dnd41	blood
8	chr15:38843400-38848200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
9	chr15:38843400-38849800	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr15:38843600-38846800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr15:38844400-38847400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
12	chr15:38844600-38850200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:38844800-38854600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr15:38845200-38847800	Genic enhancers	Fetal Thymus	thymus
15	chr15:38845200-38847800	Genic enhancers	Thymus	Thymus
16	chr15:38845200-38848200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:38845200-38848400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:38845200-38854200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:38845400-38849000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr15:38845600-38847600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:38845800-38849600	Enhancers	Fetal Kidney	kidney
22	chr15:38845800-38852000	Weak transcription	Stomach Mucosa	stomach
23	chr15:38846000-38847200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr15:38846000-38847800	Enhancers	Brain Anterior Caudate	brain
25	chr15:38846000-38848000	Weak transcription	Fetal Brain Male	brain
26	chr15:38846000-38848000	Weak transcription	Fetal Intestine Large	intestine
27	chr15:38846000-38848000	Weak transcription	HSMM	muscle
28	chr15:38846200-38846800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr15:38846200-38846800	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr15:38846200-38846800	Enhancers	Brain Cingulate Gyrus	brain
31	chr15:38846200-38846800	Enhancers	GM12878-XiMat	blood
32	chr15:38846200-38847200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:38846200-38847200	Enhancers	Brain Hippocampus Middle	brain
34	chr15:38846200-38847400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
35	chr15:38846200-38847800	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr15:38846200-38851000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:38846400-38846800	Weak transcription	Fetal Brain Female	brain
38	chr15:38846400-38847200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr15:38846400-38847400	Genic enhancers	Primary B cells from cord blood	blood
40	chr15:38846400-38847400	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr15:38846400-38848400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:38846400-38850800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:38846600-38847200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:38846600-38847200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr15:38846600-38848200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:38846600-38848400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr15:38846600-38849600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood

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