Variant report

Variant	rs895894
Chromosome Location	chr3:135955443-135955444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:135953105..135954994-chr3:135955237..135956991,2	MCF-7	breast:
2	chr3:135954886..135956782-chr3:136102988..136105563,2	MCF-7	breast:
3	chr3:135955194..135957382-chr3:135967889..135969974,2	MCF-7	breast:
4	chr3:135914260..135917175-chr3:135955428..135961207,5	MCF-7	breast:
5	chr3:135954969..135958105-chr3:135968052..135971178,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114054	Chromatin interaction
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10935177	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10935182	0.81[JPT][hapmap]
rs10935184	0.86[JPT][hapmap]
rs1145106	0.81[JPT][hapmap]
rs1153870	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1153872	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1153877	0.82[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1154988	1.00[JPT][hapmap]
rs1278493	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1279086	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1279425	0.86[JPT][hapmap]
rs1279831	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1279840	0.86[JPT][hapmap]
rs1279949	0.83[ASN][1000 genomes]
rs1711171	0.86[JPT][hapmap]
rs2459412	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2655008	0.81[JPT][hapmap]
rs3755636	0.86[JPT][hapmap]
rs3957816	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678428	0.86[JPT][hapmap]
rs483465	0.86[JPT][hapmap]
rs518972	0.89[CHD][hapmap];0.86[JPT][hapmap]
rs521746	0.83[CHD][hapmap]
rs548288	0.86[JPT][hapmap]
rs556788	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs570621	0.83[ASN][1000 genomes]
rs571513	0.86[JPT][hapmap]
rs576771	0.81[JPT][hapmap]
rs589092	0.86[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs590198	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606725	0.86[JPT][hapmap]
rs619605	0.81[JPT][hapmap]
rs632251	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634559	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs642075	0.83[ASN][1000 genomes]
rs645040	1.00[JPT][hapmap]
rs650326	0.86[JPT][hapmap]
rs654237	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs655836	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs661739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667920	0.86[JPT][hapmap]
rs668437	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs684195	0.83[ASN][1000 genomes]
rs684773	1.00[JPT][hapmap]
rs687339	1.00[JPT][hapmap]
rs695983	0.81[JPT][hapmap]
rs696081	0.89[CHD][hapmap];0.86[JPT][hapmap]
rs696516	0.81[JPT][hapmap]
rs696518	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs696520	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs698270	0.81[JPT][hapmap]
rs7372313	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9810089	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9811753	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9840812	1.00[JPT][hapmap]
rs9845457	1.00[JPT][hapmap]

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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2760738	chr3:135943988-135957333	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs895894	PPP2R3A	cis	cerebellum	SCAN
rs895894	SPSB4	cis	cerebellum	SCAN
rs895894	PCCB	cis	lymphoblastoid	seeQTL
rs895894	DBR1	cis	cerebellum	SCAN
rs895894	PPP2R3A	cis	parietal	SCAN
rs895894	PCCB	cis	cerebellum	SCAN
rs895894	PCCB	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135954600-135956000	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr3:135954600-135958400	Enhancers	HepG2	liver
3	chr3:135954800-135955800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:135955000-135955600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr3:135955000-135956600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:135955000-135956600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:135955200-135956400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:135955400-135955800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:135955400-135956000	Weak transcription	Liver	Liver

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