Variant report

Variant	rs11211366
Chromosome Location	chr1:47276242-47276243
allele	C/G
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	CEBPB	chr1:47275979-47276251	K562	blood:	n/a	chr1:47276116-47276125 chr1:47276116-47276125 chr1:47276114-47276125 chr1:47276116-47276125 chr1:47276114-47276127 chr1:47276116-47276127 chr1:47276116-47276125
2	CEBPB	chr1:47275993-47276259	HepG2	liver:	n/a	chr1:47276116-47276125 chr1:47276116-47276125 chr1:47276114-47276125 chr1:47276116-47276125 chr1:47276114-47276127 chr1:47276116-47276127 chr1:47276116-47276125

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47266762..47268483-chr1:47274674..47276282,2	MCF-7	breast:
2	chr1:47275758..47278616-chr1:47280662..47283634,2	K562	blood:

Variant related genes	Relation type
CYP4B1	TF binding region
ENSG00000142973	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11576162	0.92[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs12410657	0.86[ASN][1000 genomes]
rs1572603	0.85[ASN][1000 genomes]
rs1890250	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1890251	0.88[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2065996	1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs2185032	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs2405335	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766196	0.92[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap]
rs3766197	0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs3820080	0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs45563134	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646482	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646486	0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs4646487	0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs4646492	0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs4646493	0.92[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap]
rs4646495	0.92[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap]
rs4660960	0.86[ASN][1000 genomes]
rs668770	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs681840	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72637963	0.84[ASN][1000 genomes]
rs751027	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs837395	0.80[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1011086	chr1:47259078-47305191	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv870538	chr1:47259138-47309265	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1010063	chr1:47264205-47285118	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1004143	chr1:47270942-47321982	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1004246	chr1:47274901-47321982	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11211366	HECTD3	cis	cerebellum	SCAN
rs11211366	C1orf50	cis	parietal	SCAN
rs11211366	TXNIP	trans	brain	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47265600-47279200	Weak transcription	Gastric	stomach
2	chr1:47273400-47285600	Weak transcription	Spleen	Spleen
3	chr1:47273600-47276400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:47273600-47276400	Weak transcription	Right Atrium	heart
5	chr1:47273600-47276400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:47275600-47278200	Enhancers	Left Ventricle	heart
7	chr1:47275800-47277800	Weak transcription	Psoas Muscle	Psoas
8	chr1:47276000-47277600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:47276000-47278000	Enhancers	Adipose Nuclei	Adipose
10	chr1:47276000-47278000	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr1:47276200-47276400	Enhancers	Lung	lung
12	chr1:47276200-47277000	Genic enhancers	Esophagus	oesophagus
13	chr1:47276200-47278600	Enhancers	Right Ventricle	heart

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