Variant report

Variant	rs9378928
Chromosome Location	chr6:5068525-5068526
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	JUN	chr6:5068356-5068944	HepG2	liver:	n/a	chr6:5068750-5068763 chr6:5068754-5068763
2	RXRA	chr6:5068134-5068873	HepG2	liver:	n/a	chr6:5068507-5068521
3	MXI1	chr6:5068222-5068937	HepG2	liver:	n/a	n/a
4	MYBL2	chr6:5068025-5069078	HepG2	liver:	n/a	n/a
5	MAZ	chr6:5068329-5068845	HepG2	liver:	n/a	n/a
6	JUND	chr6:5068288-5068924	HepG2	liver:	n/a	chr6:5068754-5068763
7	MYC	chr6:5068413-5068791	HepG2	liver:	n/a	n/a
8	REST	chr6:5068203-5068919	HepG2	liver:	n/a	n/a
9	SMC3	chr6:5068121-5068904	HepG2	liver:	n/a	n/a
10	ZBTB7A	chr6:5068367-5068936	HepG2	liver:	n/a	n/a
11	HNF4A	chr6:5068266-5068910	HepG2	liver:	n/a	chr6:5068451-5068466
12	HNF4G	chr6:5068203-5068900	HepG2	liver:	n/a	chr6:5068451-5068466
13	EP300	chr6:5068272-5069002	HepG2	liver:	n/a	chr6:5068514-5068524 chr6:5068295-5068309
14	RAD21	chr6:5068267-5068881	HepG2	liver:	n/a	n/a
15	FOSL2	chr6:5068248-5068993	HepG2	liver:	n/a	chr6:5068754-5068763
16	ELF1	chr6:5068266-5068917	HepG2	liver:	n/a	n/a
17	RAD21	chr6:5068318-5068794	HepG2	liver:	n/a	n/a
18	FOXA1	chr6:5068057-5069046	HepG2	liver:	n/a	n/a
19	MBD4	chr6:5068060-5069059	HepG2	liver:	n/a	n/a
20	CTCF	chr6:5068451-5068531	HepG2	liver:	n/a	n/a
21	HNF4A	chr6:5068194-5068899	HepG2	liver:	n/a	chr6:5068451-5068466
22	CTCF	chr6:5068374-5068674	HepG2	liver:	n/a	n/a
23	CEBPB	chr6:5068292-5068755	HepG2	liver:	n/a	n/a
24	MAX	chr6:5067495-5069151	HepG2	liver:	n/a	chr6:5068871-5068879
25	EP300	chr6:5068153-5068948	HepG2	liver:	n/a	chr6:5068514-5068524 chr6:5068295-5068309
26	NFIC	chr6:5068038-5069019	HepG2	liver:	n/a	chr6:5068673-5068701
27	FOXA1	chr6:5068086-5068971	HepG2	liver:	n/a	n/a
28	CTCF	chr6:5068440-5068590	Caco-2	colon:	n/a	n/a
29	EP300	chr6:5068261-5068903	HepG2	liver:	n/a	chr6:5068514-5068524 chr6:5068295-5068309
30	MAFF	chr6:5068305-5068834	HepG2	liver:	n/a	n/a
31	HDAC2	chr6:5068178-5068989	HepG2	liver:	n/a	chr6:5068630-5068649 chr6:5068295-5068309 chr6:5068515-5068524
32	MAFK	chr6:5068203-5068850	HepG2	liver:	n/a	n/a
33	FOXA2	chr6:5067657-5069164	HepG2	liver:	n/a	n/a
34	MAX	chr6:5068199-5069069	HepG2	liver:	n/a	chr6:5068871-5068879
35	CREB1	chr6:5068134-5069127	HepG2	liver:	n/a	chr6:5068752-5068765
36	BHLHE40	chr6:5068350-5068896	HepG2	liver:	n/a	chr6:5068537-5068553
37	MAFK	chr6:5068282-5068836	HepG2	liver:	n/a	n/a
38	CEBPD	chr6:5068332-5068958	HepG2	liver:	n/a	n/a
39	FOXA2	chr6:5068205-5068942	HepG2	liver:	n/a	n/a
40	NFIC	chr6:5068111-5068980	HepG2	liver:	n/a	chr6:5068673-5068701
41	TBP	chr6:5068250-5068843	HepG2	liver:	n/a	n/a
42	RFX5	chr6:5068388-5068923	HepG2	liver:	n/a	n/a
43	JUND	chr6:5068298-5068875	HepG2	liver:	n/a	chr6:5068754-5068763
44	TCF12	chr6:5068291-5068947	HepG2	liver:	n/a	chr6:5068393-5068402
45	CHD2	chr6:5068338-5068924	HepG2	liver:	n/a	n/a
46	HEY1	chr6:5068264-5069047	HepG2	liver:	n/a	chr6:5068753-5068762 chr6:5068755-5068764
47	CTCF	chr6:5068380-5068530	HepG2	liver:	n/a	n/a
48	TEAD4	chr6:5068121-5069019	HepG2	liver:	n/a	n/a
49	YY1	chr6:5068287-5068888	HepG2	liver:	n/a	chr6:5068597-5068608 chr6:5068520-5068529
50	RXRA	chr6:5068222-5068944	HepG2	liver:	n/a	chr6:5068507-5068521

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5067584..5069589-chr6:5073200..5075622,2	MCF-7	breast:
2	chr6:5067420..5070838-chr6:5082550..5086486,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000220685	TF binding region
ENSG00000219607	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11242988	1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1265347	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1265351	0.88[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs13340416	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs200852	0.91[CHD][hapmap]
rs200853	0.91[CHD][hapmap]
rs200854	0.91[CHD][hapmap]
rs200856	0.91[CHD][hapmap]
rs374283	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs376210	0.86[ASN][1000 genomes]
rs378259	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs379169	0.92[ASN][1000 genomes]
rs398302	0.81[ASN][1000 genomes]
rs421273	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs425133	0.96[ASN][1000 genomes]
rs441144	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs449288	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs450634	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7752352	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7752365	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9378416	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9378930	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9378931	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9378932	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9378933	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9392071	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9392649	0.86[EUR][1000 genomes]
rs9392650	0.91[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9392651	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9392653	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9405254	0.91[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs9405255	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9405256	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1024028	chr6:5057399-5081990	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv427744	chr6:5061006-5073109	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1017373	chr6:5066785-5128943	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv538112	chr6:5066785-5128943	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9378928	LYRM4	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5067200-5068600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:5067400-5074000	Weak transcription	Ovary	ovary
3	chr6:5067600-5068800	Enhancers	Liver	Liver
4	chr6:5067800-5071200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:5068000-5068600	Weak transcription	Fetal Intestine Small	intestine
6	chr6:5068200-5068800	Enhancers	Fetal Intestine Large	intestine
7	chr6:5068200-5069000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr6:5068200-5069000	Flanking Active TSS	HepG2	liver

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