Variant report

Variant	rs625045
Chromosome Location	chr1:85434613-85434614
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	chr1:85434009..85435841-chr1:85437123..85439359,2	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10782534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10782536	1.00[CEU][hapmap];0.91[GIH][hapmap];0.88[EUR][1000 genomes]
rs10873669	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873670	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873672	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873676	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873677	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873678	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10873679	1.00[CEU][hapmap];0.91[GIH][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10873682	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs10873683	0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs11161495	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161496	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11161498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11161499	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11161501	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161502	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161503	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161504	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161505	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161513	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11161514	0.96[CEU][hapmap];0.89[GIH][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs11485283	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11485284	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11799517	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11804248	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12022421	1.00[CEU][hapmap];0.86[GIH][hapmap]
rs12062414	1.00[CEU][hapmap]
rs12091131	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12130357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12138711	0.87[EUR][1000 genomes]
rs12730688	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12754569	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1439130	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1837328	0.84[EUR][1000 genomes]
rs2389792	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2389793	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2486755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3850430	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3861690	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3895846	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3904965	0.82[ASN][1000 genomes]
rs486751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs488710	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4907017	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907018	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907118	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4907123	0.81[EUR][1000 genomes]
rs4907125	0.85[EUR][1000 genomes]
rs495786	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs499539	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs513430	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs515303	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs530486	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs531423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs589653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs600536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs603746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631267	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs632545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs648660	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs650529	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs651916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6576736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs662948	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6677091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6685363	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs668860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691674	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6691970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6700622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs677476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs679167	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726708	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7516329	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7516610	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7516625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7519134	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7522851	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7541684	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7549346	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7552445	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7553886	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs625045	MCOLN2	cis	Artery Tibial	GTEx
rs625045	MCOLN2	cis	multi-tissue	Pritchard
rs625045	NA	cis	multi-tissue	Pritchard
rs625045	MCOLN2	cis	Thyroid	GTEx
rs625045	MCOLN2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85416200-85435400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr1:85425600-85435200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:85431400-85435400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr1:85431400-85437600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:85434200-85435000	Genic enhancers	GM12878-XiMat	blood
6	chr1:85434400-85436600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:85434600-85435400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:85434600-85435600	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr1:85434600-85437400	Weak transcription	Fetal Intestine Large	intestine
10	chr1:85434600-85437400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:85434600-85437800	Weak transcription	Fetal Intestine Small	intestine

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