Variant report

Variant	rs12948881
Chromosome Location	chr17:19637540-19637541
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr17:19637347-19638474	A549	lung:	n/a	n/a
2	HDAC2	chr17:19637158-19637722	HepG2	liver:	n/a	n/a
3	RAD21	chr17:19637234-19637668	HepG2	liver:	n/a	n/a
4	MBD4	chr17:19637344-19637798	HepG2	liver:	n/a	n/a
5	POLR2A	chr17:19636604-19639167	A549	lung:	n/a	n/a
6	NFIC	chr17:19637192-19637797	HepG2	liver:	n/a	n/a
7	CEBPB	chr17:19637381-19637655	HepG2	liver:	n/a	n/a
8	FOXA1	chr17:19637211-19637854	HepG2	liver:	n/a	n/a
9	FOXA2	chr17:19637139-19637982	HepG2	liver:	n/a	n/a
10	HEY1	chr17:19637443-19637789	HepG2	liver:	n/a	n/a
11	SMC3	chr17:19637404-19637735	HepG2	liver:	n/a	n/a
12	TCF12	chr17:19637212-19639199	A549	lung:	n/a	n/a
13	FOXA2	chr17:19637287-19637809	A549	lung:	n/a	n/a
14	SIN3AK20	chr17:19637189-19637761	MCF-7	breast:	n/a	n/a
15	HNF4G	chr17:19637223-19637864	HepG2	liver:	n/a	chr17:19637523-19637538
16	POLR2A	chr17:19637464-19637793	HepG2	liver:	n/a	n/a
17	MAFK	chr17:19637437-19637747	HepG2	liver:	n/a	n/a
18	RFX5	chr17:19637459-19637659	HepG2	liver:	n/a	n/a
19	NFIC	chr17:19637206-19637801	HepG2	liver:	n/a	n/a
20	HNF4G	chr17:19637233-19637754	HepG2	liver:	n/a	chr17:19637523-19637538
21	MAX	chr17:19637148-19637844	HepG2	liver:	n/a	n/a
22	MYBL2	chr17:19637157-19638107	HepG2	liver:	n/a	n/a
23	EP300	chr17:19637349-19637838	HepG2	liver:	n/a	n/a
24	HNF4A	chr17:19637389-19637687	HepG2	liver:	n/a	chr17:19637524-19637539
25	FOXA1	chr17:19637186-19638021	HepG2	liver:	n/a	n/a
26	SP1	chr17:19637301-19637823	A549	lung:	n/a	n/a
27	MAFK	chr17:19637404-19637591	HepG2	liver:	n/a	n/a
28	TEAD4	chr17:19637165-19637811	HepG2	liver:	n/a	n/a
29	MAX	chr17:19637413-19637614	HepG2	liver:	n/a	n/a
30	FOXA1	chr17:19637189-19637820	HepG2	liver:	n/a	n/a
31	HDAC2	chr17:19637157-19637678	HepG2	liver:	n/a	n/a
32	TBP	chr17:19637426-19637676	HepG2	liver:	n/a	n/a
33	MYBL2	chr17:19637148-19637871	HepG2	liver:	n/a	n/a
34	HNF4A	chr17:19637270-19637754	HepG2	liver:	n/a	chr17:19637524-19637539
35	EP300	chr17:19637157-19637807	HepG2	liver:	n/a	n/a
36	JUND	chr17:19637350-19637664	HepG2	liver:	n/a	n/a
37	FOXA1	chr17:19637154-19638109	HepG2	liver:	n/a	n/a
38	ARID3A	chr17:19637219-19637777	HepG2	liver:	n/a	n/a
39	RXRA	chr17:19637201-19637689	HepG2	liver:	n/a	n/a
40	NR2F2	chr17:19637238-19637838	HepG2	liver:	n/a	n/a
41	RAD21	chr17:19637384-19637634	HepG2	liver:	n/a	n/a
42	SP1	chr17:19637202-19637892	HepG2	liver:	n/a	n/a
43	MAZ	chr17:19637353-19637684	HepG2	liver:	n/a	n/a
44	BCL3	chr17:19637261-19639226	A549	lung:	n/a	n/a
45	FOXA2	chr17:19637281-19637999	A549	lung:	n/a	n/a
46	TCF7L2	chr17:19637272-19637684	HepG2	liver:	n/a	n/a
47	FOXA2	chr17:19637182-19637893	HepG2	liver:	n/a	n/a
48	EP300	chr17:19637157-19637776	HepG2	liver:	n/a	n/a
49	NR2F2	chr17:19637286-19637868	MCF-7	breast:	n/a	n/a
50	JUND	chr17:19637355-19637595	HepG2	liver:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19634897..19636711-chr17:19636804..19638425,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000264785	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1006553	0.92[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1042183	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650088	0.92[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11651480	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11653719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655457	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11656096	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs11657205	0.80[TSI][hapmap]
rs12945000	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17720157	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1989379	0.86[GIH][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs2016823	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072329	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2072330	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3760486	0.96[CEU][hapmap];0.94[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3760487	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3786036	0.80[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3826507	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv907866	chr17:19582533-19697976	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv1807724	chr17:19597423-19656009	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv907867	chr17:19603060-19697976	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv1793043	chr17:19604821-19670329	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv526290	chr17:19613357-19651482	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv457704	chr17:19620477-19663747	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv470582	chr17:19620477-19663747	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv574580	chr17:19620477-19663747	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12948881	FLJ10847	cis	multi-tissue	Pritchard
rs12948881	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs12948881	ALDH3A2	cis	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19623200-19648400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr17:19628200-19640800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr17:19631800-19637600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr17:19631800-19639400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr17:19632000-19648000	Weak transcription	Spleen	Spleen
6	chr17:19632200-19637600	Weak transcription	Small Intestine	intestine
7	chr17:19632200-19640400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:19633200-19639600	Weak transcription	Gastric	stomach
9	chr17:19633600-19638600	Weak transcription	Ovary	ovary
10	chr17:19634200-19637600	Enhancers	HepG2	liver
11	chr17:19634800-19640800	Weak transcription	Esophagus	oesophagus
12	chr17:19635200-19638800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr17:19635400-19647800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr17:19636800-19638600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr17:19636800-19641200	Enhancers	Fetal Intestine Large	intestine
16	chr17:19636800-19641600	Enhancers	Fetal Intestine Small	intestine
17	chr17:19637000-19640200	Enhancers	Stomach Mucosa	stomach
18	chr17:19637200-19637800	Weak transcription	Colonic Mucosa	Colon
19	chr17:19637200-19637800	Enhancers	A549	lung
20	chr17:19637400-19640000	Enhancers	Duodenum Mucosa	Duodenum

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