Variant report

Variant	rs4123223
Chromosome Location	chr1:85465026-85465027
allele	C/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	MTA3	chr1:85464165-85465112	GM12878	blood:	n/a	n/a
3	WRNIP1	chr1:85464037-85465106	GM12878	blood:	n/a	n/a
4	SUZ12	chr1:85461677-85465137	NT2-D1	testis:	n/a	n/a

Variant related genes	Relation type
MCOLN2	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11161500	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11799554	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11800103	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12119445	0.80[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap]
rs12129308	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12130357	0.88[YRI][hapmap]
rs12140467	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12146119	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2031480	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3754270	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs3850429	0.98[ASN][1000 genomes]
rs472373	0.92[EUR][1000 genomes]
rs473957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4907015	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs498429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs504504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs507465	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs521435	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs522195	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs536609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs541897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs550766	0.92[EUR][1000 genomes]
rs574954	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs591772	0.88[EUR][1000 genomes]
rs593721	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs593745	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs597630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs597704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs600924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs613190	0.92[EUR][1000 genomes]
rs615161	0.92[EUR][1000 genomes]
rs632623	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs640149	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs645435	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs652272	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs654662	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs654666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs657309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs658658	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs666515	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs668263	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs671852	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs672202	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs673998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs674182	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs674647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67529032	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs688208	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7516625	0.89[YRI][hapmap]
rs7522851	0.85[MKK][hapmap]
rs7537383	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4123223	MCOLN2	cis	lymphoblastoid	seeQTL
rs4123223	MCOLN2	cis	Lymphoblastoid	GTEx
rs4123223	MCOLN2	cis	Thyroid	GTEx
rs4123223	WDR63	cis	parietal	SCAN
rs4123223	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL
rs4123223	MCOLN2	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85464200-85467000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:85464400-85466800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:85464600-85465200	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr1:85464600-85465200	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:85464800-85465200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr1:85464800-85465200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:85464800-85465400	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:85464800-85466800	Active TSS	GM12878-XiMat	blood
9	chr1:85465000-85465200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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