Variant report

Variant	rs17574546
Chromosome Location	chr15:38902476-38902477
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:38901614..38903345-chr15:38906817..38909369,2	MCF-7	breast:
2	chr15:38900766..38902547-chr15:38915124..38917930,2	MCF-7	breast:
3	chr15:38902462..38904762-chr15:38908656..38911078,2	MCF-7	breast:
4	chr15:38884414..38892257-chr15:38898196..38905033,11	MCF-7	breast:
5	chr15:38894183..38896835-chr15:38901481..38902998,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10520096	0.99[AFR][1000 genomes]
rs16967103	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16967104	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16967112	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16967120	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17651741	0.95[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs17652674	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17653133	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4614699	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55762999	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55791667	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56083426	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56165729	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56249992	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56279249	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60455438	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60924694	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61109886	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61573680	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171171	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72729306	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72729314	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72729320	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72729321	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72729322	0.81[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17574546	C15orf54	cis	parietal	SCAN
rs17574546	RP11-102L12.2	cis	Esophagus Mucosa	GTEx
rs17574546	RP11-275I4.2	cis	Esophagus Mucosa	GTEx
rs17574546	C15orf41	cis	cerebellum	SCAN
rs17574546	ARHGAP11A	cis	parietal	SCAN
rs17574546	EIF2AK4	cis	parietal	SCAN
rs17574546	RASGRP1	cis	normal skin	skin_eQTL
rs17574546	RASGRP1	cis	Esophagus Mucosa	GTEx
rs17574546	RASGRP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38886800-38902600	Weak transcription	Primary T cells from cord blood	blood
2	chr15:38891000-38902600	Weak transcription	Thymus	Thymus
3	chr15:38896400-38903400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:38898600-38903000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:38899800-38903000	Weak transcription	K562	blood
6	chr15:38901000-38903800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:38901200-38903000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr15:38901200-38903000	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr15:38901200-38903200	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr15:38901200-38905600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr15:38901200-38905800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr15:38901200-38905800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr15:38901200-38905800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr15:38901200-38906000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:38901200-38913400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:38901400-38903200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr15:38901600-38903400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:38901600-38903400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:38901600-38904600	Enhancers	Primary B cells from peripheral blood	blood
20	chr15:38901800-38902600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:38901800-38903200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:38902200-38906000	Enhancers	Fetal Thymus	thymus
23	chr15:38902400-38904200	Enhancers	Primary B cells from cord blood	blood

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