Variant report

Variant	rs9874493
Chromosome Location	chr3:133668539-133668540
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	ZNF263	chr3:133668283-133668678	HEK293-T-REx	kidney:	n/a	n/a
2	STAT3	chr3:133668448-133668648	MCF10A-Er-Src	breast:	n/a	chr3:133668458-133668469
3	CTBP2	chr3:133668215-133668614	H1-hESC	embryonic stem cell:	n/a	n/a
4	MYC	chr3:133668483-133668667	MCF10A-Er-Src	breast:	n/a	n/a
5	NFIC	chr3:133668179-133668686	ECC-1	luminal epithelium:	n/a	n/a
6	NFIC	chr3:133668206-133668688	ECC-1	luminal epithelium:	n/a	n/a
7	NANOG	chr3:133668272-133668589	H1-hESC	embryonic stem cell:	n/a	chr3:133668458-133668467
8	MAX	chr3:133668370-133668617	H1-hESC	embryonic stem cell:	n/a	n/a
9	NANOG	chr3:133668337-133668652	H1-hESC	embryonic stem cell:	n/a	chr3:133668458-133668467
10	FOS	chr3:133668394-133668613	MCF10A-Er-Src	breast:	n/a	n/a
11	RAD21	chr3:133668323-133668641	SK-N-SH_RA	brain:	n/a	n/a
12	MYC	chr3:133668467-133668667	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr3:133668330-133668628	MCF10A-Er-Src	breast:	n/a	chr3:133668458-133668469

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133663716..133666753-chr3:133668228..133671797,3	MCF-7	breast:

Variant related genes	Relation type
SLCO2A1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11716235	1.00[CHB][hapmap]
rs11720811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058950	1.00[CHB][hapmap]
rs13074733	1.00[CHB][hapmap]
rs13083496	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28547582	0.95[EUR][1000 genomes]
rs34087836	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34603519	0.95[EUR][1000 genomes]
rs34856813	0.95[EUR][1000 genomes]
rs35473313	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35843040	0.95[EUR][1000 genomes]
rs35911303	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075873	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241361	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs4241362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs4331673	0.82[TSI][hapmap]
rs4634113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs4643708	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56078520	0.84[EUR][1000 genomes]
rs62269155	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs7634038	1.00[CHB][hapmap]
rs7639796	1.00[CHB][hapmap]
rs9828294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs9840711	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs9855403	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9881514	1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882333	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.80[TSI][hapmap];0.87[EUR][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	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133660800-133676400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:133662600-133668600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr3:133663400-133669400	Enhancers	Spleen	Spleen
4	chr3:133663800-133694800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:133664000-133668600	Enhancers	HUVEC	blood vessel
6	chr3:133664000-133676000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:133664000-133705400	Weak transcription	Fetal Intestine Small	intestine
8	chr3:133664800-133713000	Weak transcription	Gastric	stomach
9	chr3:133665000-133673400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:133665800-133671200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:133667000-133668600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:133667000-133668600	Enhancers	Fetal Muscle Leg	muscle
13	chr3:133667000-133669000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:133667200-133668600	Enhancers	Esophagus	oesophagus
15	chr3:133667600-133676200	Weak transcription	Psoas Muscle	Psoas
16	chr3:133667800-133668600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:133667800-133669200	Enhancers	Fetal Muscle Trunk	muscle
18	chr3:133668000-133668600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:133668000-133668600	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr3:133668000-133668600	Enhancers	Adipose Nuclei	Adipose
21	chr3:133668000-133668800	Enhancers	Brain Germinal Matrix	brain
22	chr3:133668000-133668800	Enhancers	Fetal Stomach	stomach
23	chr3:133668000-133670200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:133668200-133668600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:133668200-133668600	Enhancers	Brain Angular Gyrus	brain
26	chr3:133668200-133668600	Enhancers	Fetal Lung	lung
27	chr3:133668200-133668600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr3:133668200-133670200	Weak transcription	Lung	lung
29	chr3:133668400-133670400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:133668400-133674800	Weak transcription	Right Ventricle	heart
31	chr3:133668400-133675200	Weak transcription	Right Atrium	heart
32	chr3:133668400-133685600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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