Variant report

Variant	rs10019751
Chromosome Location	chr4:119770915-119770916
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	chr4:119756043..119758170-chr4:119769333..119772030,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10014331	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11730732	0.92[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs11944285	0.93[ASN][1000 genomes]
rs2052769	0.95[ASN][1000 genomes]
rs28469651	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28706123	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28783784	0.94[ASN][1000 genomes]
rs6848274	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs767193	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9884928	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs992463	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][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	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3376985	chr4:119757182-119774736	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10019751	TRPC3	cis	cerebellum	SCAN
rs10019751	NUDT6	cis	cerebellum	SCAN
rs10019751	FGF2	cis	parietal	SCAN
rs10019751	PRSS12	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119758200-119771200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:119762800-119771400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:119764000-119771000	Weak transcription	NHDF-Ad	bronchial
4	chr4:119764000-119771200	Weak transcription	NHEK	skin
5	chr4:119764000-119771200	Weak transcription	Osteobl	bone
6	chr4:119764000-119771600	Weak transcription	HSMM	muscle
7	chr4:119764800-119771400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:119764800-119771600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:119764800-119771800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:119767000-119771400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:119769600-119771400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:119770000-119771000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr4:119770200-119771000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr4:119770400-119771200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:119770400-119771200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr4:119770400-119771400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:119770600-119772000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr4:119770600-119772000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr4:119770800-119771000	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr4:119770800-119771000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr4:119770800-119771200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr4:119770800-119771800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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