Variant report

Variant	rs7521837
Chromosome Location	chr1:154252860-154252861
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	chr1:153938174..153939881-chr1:154251981..154254395,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273026	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10797061	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs10908751	0.86[ASW][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap]
rs11584755	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586916	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194580	0.86[ASW][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap]
rs1194600	1.00[JPT][hapmap];0.91[YRI][hapmap]
rs1194602	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs1194603	0.86[ASW][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.81[YRI][hapmap]
rs1194604	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12063830	0.86[ASW][hapmap]
rs12142550	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354278	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13796	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2220390	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4072431	0.86[ASW][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4364874	0.86[ASW][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4393149	0.86[ASW][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.83[YRI][hapmap]
rs4579747	0.86[ASW][hapmap]
rs4845605	0.86[ASW][hapmap]
rs4845610	1.00[JPT][hapmap];0.91[YRI][hapmap]
rs61807361	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6667222	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9803862	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9804045	0.86[ASW][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap]

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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats 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	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7521837	GBA	cis	parietal	SCAN
rs7521837	SPRR4	cis	cerebellum	SCAN
rs7521837	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL
rs7521837	FAM63A	cis	cerebellum	SCAN
rs7521837	LCE1A	cis	parietal	SCAN
rs7521837	C1orf43	cis	parietal	SCAN
rs7521837	LCE1C	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154246200-154259400	Weak transcription	Right Atrium	heart
2	chr1:154246600-154253400	Weak transcription	HepG2	liver
3	chr1:154248200-154255200	Weak transcription	Pancreas	Pancrea
4	chr1:154248400-154253200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:154248400-154255000	Weak transcription	A549	lung
6	chr1:154248400-154255800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:154248400-154256800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:154248400-154261000	Weak transcription	K562	blood
9	chr1:154249400-154255000	Weak transcription	Spleen	Spleen
10	chr1:154249600-154254000	Weak transcription	Ovary	ovary
11	chr1:154249600-154255000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:154250600-154253200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:154250800-154253400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:154250800-154254000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr1:154250800-154259400	Weak transcription	Lung	lung
16	chr1:154251200-154253200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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