Variant report

Variant	rs9403521
Chromosome Location	chr6:143994199-143994200
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	MAX	chr6:143994078-143994525	ECC-1	luminal epithelium:	n/a	n/a
2	JUND	chr6:143994083-143994221	HepG2	liver:	n/a	chr6:143994140-143994151
3	JUN	chr6:143994149-143994342	H1-hESC	embryonic stem cell:	n/a	n/a
4	SP1	chr6:143994042-143994547	HCT-116	colon:	n/a	chr6:143994303-143994313 chr6:143994303-143994313
5	JUND	chr6:143993987-143994309	Hela-S3	cervix:	n/a	chr6:143994140-143994151
6	TCF12	chr6:143994020-143994459	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr6:143994054-143994542	HCT-116	colon:	n/a	n/a
8	JUN	chr6:143994015-143994336	K562	blood:	n/a	n/a
9	KAP1	chr6:143994090-143994376	U2OS	brain:	n/a	n/a
10	MYC	chr6:143994129-143994424	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr6:143993991-143994337	MCF10A-Er-Src	breast:	n/a	chr6:143994140-143994151
12	JUND	chr6:143994073-143994267	HepG2	liver:	n/a	chr6:143994140-143994151
13	FOSL1	chr6:143993888-143994412	HCT-116	colon:	n/a	n/a
14	FOXM1	chr6:143993964-143995490	ECC-1	luminal epithelium:	n/a	n/a
15	JUND	chr6:143993992-143994334	H1-hESC	embryonic stem cell:	n/a	chr6:143994140-143994151
16	FOSL1	chr6:143994051-143994539	HCT-116	colon:	n/a	n/a
17	MYC	chr6:143994169-143994541	MCF10A-Er-Src	breast:	n/a	n/a
18	FOSL2	chr6:143993970-143994334	HepG2	liver:	n/a	n/a
19	POLR2A	chr6:143994058-143994342	HCT-116	colon:	n/a	n/a
20	FOS	chr6:143993990-143994477	MCF10A-Er-Src	breast:	n/a	chr6:143994140-143994151
21	EP300	chr6:143993892-143995949	ECC-1	luminal epithelium:	n/a	chr6:143995296-143995306
22	MAX	chr6:143994076-143994518	ECC-1	luminal epithelium:	n/a	n/a
23	FOS	chr6:143993986-143994520	MCF10A-Er-Src	breast:	n/a	chr6:143994140-143994151
24	JUND	chr6:143993986-143994340	K562	blood:	n/a	chr6:143994140-143994151
25	FOS	chr6:143993994-143994321	HUVEC	blood vessel:	n/a	chr6:143994140-143994151
26	SETDB1	chr6:143994013-143994406	U2OS	brain:	n/a	n/a
27	GTF2F1	chr6:143994170-143994267	Hela-S3	cervix:	n/a	n/a
28	CBX3	chr6:143994061-143994516	HCT-116	colon:	n/a	n/a
29	EGR1	chr6:143994063-143994287	K562	blood:	n/a	n/a
30	FOS	chr6:143993990-143994277	MCF10A-Er-Src	breast:	n/a	chr6:143994140-143994151
31	JUND	chr6:143993984-143994290	HepG2	liver:	n/a	chr6:143994140-143994151
32	CEBPB	chr6:143994094-143995421	HCT-116	colon:	n/a	n/a
33	JUN	chr6:143994054-143994482	K562	blood:	n/a	n/a
34	JUND	chr6:143994092-143994213	H1-hESC	embryonic stem cell:	n/a	chr6:143994140-143994151
35	POLR2A	chr6:143994060-143994366	ECC-1	luminal epithelium:	n/a	n/a
36	EGR1	chr6:143993888-143994486	HCT-116	colon:	n/a	n/a
37	JUND	chr6:143993891-143994573	HCT-116	colon:	n/a	chr6:143994140-143994151
38	FOSL1	chr6:143994040-143994336	K562	blood:	n/a	n/a
39	JUND	chr6:143994048-143994524	HCT-116	colon:	n/a	chr6:143994140-143994151

No.	Distal block	Cell Line	Cell type
1	chr6:143993420..143996184-chr6:143997864..144000506,3	MCF-7	breast:
2	chr6:143993920..143996702-chr6:144021547..144023983,2	MCF-7	breast:
3	chr6:143993282..143995063-chr6:144073784..144075986,2	MCF-7	breast:

Variant related genes	Relation type
PHACTR2	TF binding region
ENSG00000112419	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10872562	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1108314	1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.92[ASN][1000 genomes]
rs11155315	0.86[CHB][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs11155317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12198291	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12206069	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12207002	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12208927	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12528456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3924969	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6901659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6907410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6913134	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.86[ASN][1000 genomes]
rs6915784	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6931801	0.86[GIH][hapmap]
rs7740709	0.84[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs7741424	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7748882	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs7766510	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7772565	0.86[CHB][hapmap];0.80[CHD][hapmap];0.87[MEX][hapmap];0.80[ASN][1000 genomes]
rs7776119	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8180640	0.91[ASN][1000 genomes]
rs9373396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9373397	0.94[JPT][hapmap]
rs9376776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9376779	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9386042	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs9386043	0.94[JPT][hapmap]
rs9390126	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9399458	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9403523	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9496739	0.86[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1032369	chr6:143925374-144007513	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv604805	chr6:143930404-144005949	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143980800-143994200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:143981800-143994200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:143991400-143994200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:143993400-143995600	Weak transcription	Aorta	Aorta
5	chr6:143993600-143994200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr6:143993600-143994400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:143993600-143994600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr6:143993600-143996400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr6:143993600-143996800	Enhancers	Placenta	Placenta
10	chr6:143994000-143994200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr6:143994000-143994200	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr6:143994000-143994200	Enhancers	A549	lung
13	chr6:143994000-143994200	Enhancers	NHEK	skin
14	chr6:143994000-143994400	Enhancers	Esophagus	oesophagus
15	chr6:143994000-143994600	Enhancers	HUVEC	blood vessel
16	chr6:143994000-143996200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:143994000-143997800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:143994000-143998800	Enhancers	Hela-S3	cervix

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