Variant report

Variant	rs351184
Chromosome Location	chr15:74598258-74598259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74412284..74415144-chr15:74598064..74600098,2	MCF-7	breast:
2	chr15:74594700..74596625-chr15:74596694..74599231,2	K562	blood:

Variant related genes	Relation type
ENSG00000261384	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11072478	0.83[MEX][hapmap]
rs11631552	0.87[EUR][1000 genomes]
rs11634685	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856695	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12905100	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12906092	0.84[CEU][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs12913522	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12917295	0.87[CEU][hapmap]
rs1484210	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1809500	0.84[EUR][1000 genomes]
rs2277602	0.84[MEX][hapmap]
rs2279378	0.92[CEU][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2899825	0.83[JPT][hapmap]
rs2930291	0.92[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2930302	0.83[MEX][hapmap]
rs2959004	0.84[MEX][hapmap]
rs2959008	0.83[MEX][hapmap]
rs2959011	0.92[MEX][hapmap]
rs351189	0.81[EUR][1000 genomes]
rs397074	0.87[EUR][1000 genomes]
rs413150	0.82[EUR][1000 genomes]
rs4887131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887132	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887134	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs900799	0.80[CEU][hapmap]
rs900801	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs351184	RPLP1	cis	parietal	SCAN
rs351184	SEMA7A	cis	cerebellum	SCAN
rs351184	CYP1A1	cis	cerebellum	SCAN
rs351184	ITGA11	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74584200-74607400	Weak transcription	Right Atrium	heart
2	chr15:74593800-74601000	Enhancers	Fetal Brain Female	brain
3	chr15:74593800-74601800	Enhancers	Fetal Brain Male	brain
4	chr15:74594000-74602000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr15:74596600-74600400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:74596600-74606600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:74596600-74609800	Weak transcription	A549	lung
8	chr15:74596800-74598600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:74597200-74598400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:74597200-74598600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:74597200-74598600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:74597200-74598600	Weak transcription	Spleen	Spleen
13	chr15:74597200-74599000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:74597800-74599800	Weak transcription	Brain Germinal Matrix	brain
15	chr15:74597800-74600800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr15:74598200-74601400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:74598200-74602000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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