Variant report

Variant	rs4076363
Chromosome Location	chr18:45665230-45665231
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	NFIC	chr18:45664862-45666539	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr18:45664956-45666429	ECC-1	luminal epithelium:	n/a	chr18:45665586-45665593 chr18:45666411-45666418 chr18:45666097-45666104 chr18:45665540-45665547
3	EP300	chr18:45664786-45666605	ECC-1	luminal epithelium:	n/a	chr18:45666509-45666519 chr18:45665252-45665262 chr18:45666229-45666238
4	FOXA1	chr18:45664906-45665320	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr18:45664987-45666533	ECC-1	luminal epithelium:	n/a	chr18:45665586-45665593 chr18:45666510-45666519 chr18:45666411-45666418 chr18:45666097-45666104 chr18:45665540-45665547
6	NFIC	chr18:45664718-45666531	ECC-1	luminal epithelium:	n/a	n/a
7	ZNF263	chr18:45664861-45666532	HEK293-T-REx	kidney:	n/a	chr18:45665981-45665990 chr18:45666270-45666279 chr18:45666273-45666282 chr18:45665711-45665732 chr18:45666276-45666285

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:45658580..45662145-chr18:45664603..45667810,4	MCF-7	breast:
2	chr18:45641054..45643566-chr18:45664134..45666648,2	MCF-7	breast:

Variant related genes	Relation type
ZBTB7C	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12965052	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4076364	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4078130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs61322349	0.96[ASN][1000 genomes]
rs6507818	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7243021	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7243437	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8091725	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8092444	0.81[CHB][hapmap]
rs8098626	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9951415	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9953845	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909616	chr18:45467806-45844500	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4076363	CXXC1	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45663600-45665600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:45663600-45666000	Weak transcription	Left Ventricle	heart
3	chr18:45663600-45666200	Weak transcription	Psoas Muscle	Psoas
4	chr18:45663600-45667400	Enhancers	Placenta	Placenta
5	chr18:45663600-45667400	Enhancers	Spleen	Spleen
6	chr18:45663800-45665400	Weak transcription	Ovary	ovary
7	chr18:45663800-45665400	Weak transcription	Right Ventricle	heart
8	chr18:45663800-45665600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
9	chr18:45663800-45665600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
10	chr18:45663800-45665800	Weak transcription	Liver	Liver
11	chr18:45663800-45666200	Weak transcription	Right Atrium	heart
12	chr18:45663800-45666400	Enhancers	HSMMtube	muscle
13	chr18:45663800-45666600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr18:45663800-45666600	Flanking Active TSS	Hela-S3	cervix
15	chr18:45663800-45667400	Enhancers	Gastric	stomach
16	chr18:45663800-45667800	Enhancers	Esophagus	oesophagus
17	chr18:45663800-45679800	Weak transcription	Aorta	Aorta
18	chr18:45664000-45666400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr18:45664000-45667600	Enhancers	Stomach Mucosa	stomach
20	chr18:45664000-45670400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr18:45664200-45665400	Weak transcription	HMEC	breast
22	chr18:45664200-45667400	Enhancers	Colonic Mucosa	Colon
23	chr18:45664200-45667400	Enhancers	Lung	lung
24	chr18:45664400-45667400	Enhancers	Duodenum Mucosa	Duodenum
25	chr18:45664600-45667000	Enhancers	Dnd41	blood
26	chr18:45664600-45667400	Enhancers	Pancreas	Pancrea
27	chr18:45665000-45665400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
28	chr18:45665000-45665400	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr18:45665200-45665400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
30	chr18:45665200-45665400	Enhancers	Fetal Kidney	kidney
31	chr18:45665200-45665600	Bivalent Enhancer	Fetal Intestine Large	intestine
32	chr18:45665200-45665800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr18:45665200-45666200	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr18:45665200-45666200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr18:45665200-45666400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr18:45665200-45666400	Enhancers	Stomach Smooth Muscle	stomach
37	chr18:45665200-45667400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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