Variant report

Variant	rs12028736
Chromosome Location	chr1:85517011-85517012
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	TCF7L2	chr1:85515999-85517129	HEK293	kidney:	n/a	chr1:85516570-85516584
2	SETDB1	chr1:85516545-85517121	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
MCOLN3	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10443172	0.85[ASN][1000 genomes]
rs12024977	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12030837	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12037219	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12041012	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12042160	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2028304	0.85[ASN][1000 genomes]
rs2304641	0.98[ASN][1000 genomes]
rs2840050	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61768854	0.89[EUR][1000 genomes]
rs61769366	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61770879	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6665436	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6679539	0.85[ASN][1000 genomes]
rs6688354	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6700723	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7522239	0.85[ASN][1000 genomes]
rs7540706	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7547224	0.85[EUR][1000 genomes]
rs7547317	0.85[EUR][1000 genomes]
rs893618	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs898036	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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	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
2	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
3	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
4	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
5	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

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85514600-85517600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:85514800-85527400	Weak transcription	Aorta	Aorta
3	chr1:85515200-85517600	Enhancers	Dnd41	blood
4	chr1:85515600-85517200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr1:85515800-85517400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:85515800-85523400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:85516000-85517400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:85516200-85517600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:85516400-85517200	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr1:85516600-85517200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr1:85516600-85517200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr1:85516600-85517400	Enhancers	Primary T cells from cord blood	blood

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