Variant report

Variant	rs7553886
Chromosome Location	chr1:85459188-85459189
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	chr1:85457596..85460591-chr1:85461678..85464189,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153898	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10782534	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10782536	0.84[EUR][1000 genomes]
rs10873669	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873670	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873672	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10873676	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873677	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873678	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10873679	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10873682	0.82[EUR][1000 genomes]
rs10873683	0.81[EUR][1000 genomes]
rs11161495	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161496	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161497	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11161498	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161499	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161501	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161502	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161513	0.82[EUR][1000 genomes]
rs11161514	0.81[EUR][1000 genomes]
rs11485283	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11485284	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11799517	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11804248	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12091131	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12130357	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12138711	0.83[EUR][1000 genomes]
rs12730688	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12754569	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1439130	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1837328	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2389792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486755	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3850430	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3861690	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3895846	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3904965	0.88[ASN][1000 genomes]
rs486751	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs488710	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4907017	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4907018	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4907118	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4907125	0.81[EUR][1000 genomes]
rs495786	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs499539	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs513430	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs515303	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs530486	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs531423	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs589653	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs600536	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs603746	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs625045	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs631267	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs632545	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs648660	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs650529	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs651916	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6576736	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs662948	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6677091	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685363	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs668860	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6691674	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6691970	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6700622	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs677476	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs679167	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs726708	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72720523	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7516329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516610	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7516625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519134	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7522851	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7541684	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7549346	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7552445	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	esv3515392	chr1:85437980-85465392	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3515393	chr1:85437980-85465392	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7553886	MCOLN2	cis	Esophagus Muscularis	GTEx
rs7553886	MCOLN2	cis	multi-tissue	Pritchard
rs7553886	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL
rs7553886	MCOLN2	cis	Artery Aorta	GTEx
rs7553886	MCOLN2	cis	Artery Tibial	GTEx
rs7553886	MCOLN2	cis	Adipose Subcutaneous	GTEx
rs7553886	MCOLN2	cis	Thyroid	GTEx
rs7553886	MCOLN2	cis	Stomach	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85441200-85460200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:85454800-85460600	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:85454800-85461600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:85454800-85462000	Weak transcription	Spleen	Spleen
5	chr1:85454800-85462200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:85455800-85460000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:85457200-85460200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:85457200-85461800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:85457600-85459800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:85457800-85460400	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr1:85458000-85460400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr1:85458200-85461000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:85458200-85461000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr1:85459000-85459200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:85459000-85459200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:85459000-85459200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
17	chr1:85459000-85460000	Weak transcription	Primary B cells from peripheral blood	blood

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