Variant report

Variant	rs2945147
Chromosome Location	chr1:85063134-85063135
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85062635..85064532-chr1:85066699..85068510,2	K562	blood:
2	chr1:85060422..85063217-chr1:85063481..85066367,2	K562	blood:
3	chr1:85046450..85049039-chr1:85062565..85064761,2	K562	blood:
4	chr1:85038534..85040973-chr1:85062371..85064960,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117151	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10874451	1.00[CHB][hapmap]
rs11164005	0.80[GIH][hapmap]
rs12119873	0.86[EUR][1000 genomes]
rs12123470	0.84[EUR][1000 genomes]
rs12125418	0.86[CHB][hapmap]
rs12127160	0.86[EUR][1000 genomes]
rs12137275	0.80[EUR][1000 genomes]
rs12141472	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs12145771	0.85[EUR][1000 genomes]
rs1417295	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1517601	0.85[EUR][1000 genomes]
rs15911	0.80[GIH][hapmap]
rs1914477	0.86[EUR][1000 genomes]
rs2203455	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2303307	0.88[CEU][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2911591	0.86[EUR][1000 genomes]
rs2911592	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2911594	0.81[EUR][1000 genomes]
rs2911595	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2911597	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2911598	1.00[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2911599	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2911607	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2911609	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2943671	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2945143	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945145	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];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945149	0.82[ASN][1000 genomes]
rs2945153	0.85[EUR][1000 genomes]
rs2994435	0.88[EUR][1000 genomes]
rs2994934	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2994935	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2994937	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2994938	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2994943	0.91[ASN][1000 genomes]
rs2994944	0.82[ASN][1000 genomes]
rs2994947	0.88[ASN][1000 genomes]
rs2994948	0.82[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs2994953	0.83[MEX][hapmap]
rs41299545	0.86[EUR][1000 genomes]
rs4907079	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs6690204	0.86[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs7517756	0.84[EUR][1000 genomes]
rs880412	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000325	chr1:85032605-85100748	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2945147	BCL10	cis	cerebellum	SCAN
rs2945147	SPATA1	cis	parietal	SCAN
rs2945147	CTBS	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85051000-85069800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:85052000-85064600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:85062400-85063800	Enhancers	Fetal Heart	heart
4	chr1:85062600-85063200	Enhancers	Stomach Mucosa	stomach
5	chr1:85062600-85064400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:85062800-85063200	Enhancers	GM12878-XiMat	blood
7	chr1:85062800-85064400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:85062800-85066800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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