Variant report

Variant	rs726708
Chromosome Location	chr1:85464843-85464844
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:85459671-85465061	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:85461494-85464994	GM12892	blood:	n/a	n/a
3	CTCF	chr1:85464700-85464850	GM12875	blood:	n/a	n/a
4	CTCF	chr1:85464740-85464890	HAc	cerebellar:	n/a	n/a
5	CTCF	chr1:85464720-85464870	GM12865	blood:	n/a	n/a
6	CTCF	chr1:85464780-85464930	HCPEpiC	choroid plexus:	n/a	n/a
7	CTCF	chr1:85464808-85464891	GM12892	blood:	n/a	n/a
8	MTA3	chr1:85464165-85465112	GM12878	blood:	n/a	n/a
9	WRNIP1	chr1:85464037-85465106	GM12878	blood:	n/a	n/a
10	RUNX3	chr1:85464567-85464877	GM12878	blood:	n/a	n/a
11	CTCF	chr1:85464740-85464890	HCPEpiC	choroid plexus:	n/a	n/a
12	POLR2A	chr1:85464539-85464999	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:85459795-85464999	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:85460981-85465011	GM19099	blood:	n/a	n/a
15	CTCF	chr1:85464720-85464870	GM06990	blood:	n/a	n/a
16	CTCF	chr1:85464840-85464990	GM12871	blood:	n/a	n/a
17	POLR2A	chr1:85464372-85464883	GM12892	blood:	n/a	n/a
18	POLR2A	chr1:85461099-85464971	GM19193	blood:	n/a	n/a
19	CTCF	chr1:85464780-85464930	HBMEC	blood vessel:	n/a	n/a
20	CEBPB	chr1:85464587-85464939	H1-hESC	embryonic stem cell:	n/a	n/a
21	SUZ12	chr1:85461677-85465137	NT2-D1	testis:	n/a	n/a
22	CTCF	chr1:85464718-85464966	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:85461512-85464970	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:85464493-85464944	GM12892	blood:	n/a	n/a
25	NRF1	chr1:85464515-85464873	GM12878	blood:	n/a	n/a
26	SPI1	chr1:85464634-85464853	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
MCOLN2	TF binding region

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

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

rs_ID	r²[population]
rs10782534	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10782536	0.84[EUR][1000 genomes]
rs10873669	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10873670	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10873672	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873676	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873677	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873678	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10873679	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10873682	0.82[EUR][1000 genomes]
rs10873683	0.81[EUR][1000 genomes]
rs11161495	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11161496	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11161497	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11161498	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11161499	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11161501	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161502	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161503	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161504	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161505	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161513	0.82[EUR][1000 genomes]
rs11161514	0.81[EUR][1000 genomes]
rs11485283	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11485284	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11799517	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11804248	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12091131	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12130357	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12138711	0.83[EUR][1000 genomes]
rs12730688	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12754569	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1439130	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1837328	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2389792	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389793	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2486755	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3850430	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3861690	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3895846	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3904965	0.93[ASN][1000 genomes]
rs486751	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs488710	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4907017	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4907018	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4907118	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4907125	0.81[EUR][1000 genomes]
rs495786	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs499539	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs513430	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs515303	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs530486	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs531423	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs589653	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs600536	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603746	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs625045	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs631267	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs632545	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs648660	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs650529	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs651916	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6576736	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs662948	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6677091	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6685363	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs668860	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6691674	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6691970	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6700622	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs677476	0.82[EUR][1000 genomes]
rs679167	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72720523	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7516329	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7516610	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7516625	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7519134	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7522851	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7541684	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7549346	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7552445	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7553886	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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
rs726708	MCOLN2	cis	Stomach	GTEx
rs726708	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL
rs726708	MCOLN2	cis	multi-tissue	Pritchard
rs726708	MCOLN2	cis	Thyroid	GTEx
rs726708	MCOLN2	cis	Adipose Subcutaneous	GTEx
rs726708	MCOLN2	cis	Esophagus Muscularis	GTEx
rs726708	MCOLN2	cis	Artery Tibial	GTEx
rs726708	MCOLN2	cis	Artery Aorta	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85463400-85465000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
2	chr1:85464000-85465000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr1:85464200-85467000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:85464400-85465000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:85464400-85465000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:85464400-85465000	Bivalent Enhancer	NH-A	brain
7	chr1:85464400-85466800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:85464600-85465000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
9	chr1:85464600-85465000	Bivalent Enhancer	Fetal Brain Male	brain
10	chr1:85464600-85465200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr1:85464600-85465200	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:85464800-85465000	Enhancers	Primary B cells from peripheral blood	blood
13	chr1:85464800-85465000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr1:85464800-85465000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
15	chr1:85464800-85465000	Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr1:85464800-85465000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
17	chr1:85464800-85465000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:85464800-85465000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:85464800-85465000	Enhancers	Brain Anterior Caudate	brain
20	chr1:85464800-85465200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr1:85464800-85465200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:85464800-85465400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr1:85464800-85466800	Active TSS	GM12878-XiMat	blood

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