Variant report

Variant	rs2069904
Chromosome Location	chr2:128175779-128175780
allele	A/G
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	NR3C1	chr2:128175749-128176036	A549	lung:	n/a	chr2:128175890-128175916
2	HEY1	chr2:128175747-128177435	HepG2	liver:	n/a	n/a
3	HDAC2	chr2:128175654-128176798	HepG2	liver:	n/a	n/a
4	MAFK	chr2:128175680-128176609	HepG2	liver:	n/a	chr2:128176345-128176360
5	FOXA1	chr2:128175639-128177255	HepG2	liver:	n/a	n/a
6	RAD21	chr2:128175711-128176725	HepG2	liver:	n/a	chr2:128176113-128176126 chr2:128176211-128176224 chr2:128176524-128176533
7	TAF1	chr2:128175758-128176704	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:128175737-128177495	HepG2	liver:	n/a	n/a
9	NR3C1	chr2:128175761-128176032	A549	lung:	n/a	chr2:128175890-128175916
10	POLR2A	chr2:128175695-128176789	HepG2	liver:	n/a	n/a
11	NR3C1	chr2:128175707-128176158	A549	lung:	n/a	chr2:128175890-128175916
12	MYBL2	chr2:128175595-128177696	HepG2	liver:	n/a	n/a
13	CEBPD	chr2:128175744-128176733	HepG2	liver:	n/a	n/a
14	NFIC	chr2:128175695-128176874	HepG2	liver:	n/a	n/a
15	MBD4	chr2:128175663-128177420	HepG2	liver:	n/a	n/a
16	MAZ	chr2:128175772-128176499	HepG2	liver:	n/a	chr2:128176450-128176460 chr2:128176449-128176459 chr2:128176449-128176460 chr2:128176253-128176262 chr2:128176450-128176460 chr2:128176448-128176461 chr2:128176448-128176461 chr2:128176449-128176460 chr2:128176450-128176459 chr2:128176449-128176460 chr2:128176448-128176461 chr2:128176449-128176459 chr2:128176445-128176464
17	MAX	chr2:128175611-128177655	HepG2	liver:	n/a	chr2:128176450-128176460 chr2:128176449-128176459 chr2:128176449-128176460 chr2:128176253-128176262 chr2:128176450-128176460 chr2:128176448-128176461 chr2:128176448-128176461 chr2:128176449-128176460 chr2:128176450-128176459 chr2:128176449-128176460 chr2:128176448-128176461 chr2:128176449-128176459 chr2:128176445-128176464
18	SP1	chr2:128175662-128176731	HepG2	liver:	n/a	n/a
19	TEAD4	chr2:128175515-128177422	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:128175249-128180723	HepG2	liver:	n/a	n/a
21	MXI1	chr2:128175753-128176714	HepG2	liver:	n/a	chr2:128176451-128176460 chr2:128176449-128176458 chr2:128176451-128176460 chr2:128176449-128176458
22	POLR2A	chr2:128175695-128177493	HepG2	liver:	n/a	n/a
23	NFIC	chr2:128175606-128177482	HepG2	liver:	n/a	n/a
24	YY1	chr2:128175737-128176947	HepG2	liver:	n/a	chr2:128176612-128176628 chr2:128176616-128176625
25	MBD4	chr2:128175614-128177601	HepG2	liver:	n/a	n/a
26	POLR2A	chr2:128175672-128177814	HepG2	liver:	n/a	n/a
27	NR3C1	chr2:128175703-128176182	A549	lung:	n/a	chr2:128175890-128175916
28	FOXA2	chr2:128175724-128176997	HepG2	liver:	n/a	n/a
29	TAF1	chr2:128175751-128176818	HepG2	liver:	n/a	n/a
30	YY1	chr2:128175741-128176783	HepG2	liver:	n/a	chr2:128176612-128176628 chr2:128176616-128176625
31	RFX5	chr2:128175768-128176256	HepG2	liver:	n/a	n/a
32	RCOR1	chr2:128175765-128176986	HepG2	liver:	n/a	n/a
33	FOXA1	chr2:128175639-128176306	HepG2	liver:	n/a	n/a
34	REST	chr2:128175731-128176465	HepG2	liver:	n/a	n/a
35	HEY1	chr2:128175687-128177560	HepG2	liver:	n/a	n/a
36	ZBTB7A	chr2:128175768-128176703	HepG2	liver:	n/a	n/a
37	HNF4G	chr2:128175757-128176725	HepG2	liver:	n/a	chr2:128176274-128176286 chr2:128176273-128176286 chr2:128176271-128176286 chr2:128176274-128176286 chr2:128176190-128176204 chr2:128176273-128176286
38	MYBL2	chr2:128175540-128177606	HepG2	liver:	n/a	n/a
39	NR3C1	chr2:128175708-128176103	A549	lung:	n/a	chr2:128175890-128175916
40	POLR2A	chr2:128175740-128176304	HepG2	liver:	n/a	n/a
41	RAD21	chr2:128175714-128176671	HepG2	liver:	n/a	chr2:128176113-128176126 chr2:128176211-128176224 chr2:128176524-128176533
42	NR3C1	chr2:128175724-128176020	A549	lung:	n/a	chr2:128175890-128175916
43	FOXA1	chr2:128175671-128176314	HepG2	liver:	n/a	n/a
44	EP300	chr2:128175750-128176198	HepG2	liver:	n/a	n/a
45	FOXA1	chr2:128175660-128176907	HepG2	liver:	n/a	n/a
46	RAD21	chr2:128175729-128176711	HepG2	liver:	n/a	chr2:128176113-128176126 chr2:128176211-128176224 chr2:128176524-128176533
47	EP300	chr2:128175656-128176730	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128050076..128053017-chr2:128173952..128176764,3	MCF-7	breast:

Variant related genes	Relation type
PROC	TF binding region
ENSG00000163161	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1011019	1.00[CHB][hapmap];0.89[LWK][hapmap]
rs10177052	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1019842	1.00[ASN][1000 genomes]
rs10496661	0.89[LWK][hapmap];0.83[MKK][hapmap];1.00[ASN][1000 genomes]
rs10803587	1.00[CHB][hapmap]
rs10803589	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10850	1.00[CHB][hapmap];0.86[LWK][hapmap];1.00[ASN][1000 genomes]
rs1158867	0.81[MEX][hapmap]
rs11679414	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680877	1.00[ASN][1000 genomes]
rs11683986	1.00[CHB][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691088	0.82[AFR][1000 genomes]
rs11691916	1.00[ASN][1000 genomes]
rs11692990	1.00[ASN][1000 genomes]
rs13030463	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504135	1.00[ASN][1000 genomes]
rs1518760	1.00[ASN][1000 genomes]
rs1568278	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17261845	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17261859	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1820969	1.00[ASN][1000 genomes]
rs1864552	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1864554	1.00[ASN][1000 genomes]
rs2052954	1.00[ASN][1000 genomes]
rs2069895	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069902	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069919	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163345	1.00[ASN][1000 genomes]
rs2163348	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2460106	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2679409	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2896979	1.00[ASN][1000 genomes]
rs334137	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334138	1.00[ASN][1000 genomes]
rs334143	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334144	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334146	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334151	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334152	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334156	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334157	1.00[ASN][1000 genomes]
rs334158	1.00[ASN][1000 genomes]
rs334159	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334160	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3732209	0.81[ASW][hapmap];0.86[CEU][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.96[YRI][hapmap]
rs3893897	1.00[ASN][1000 genomes]
rs3958415	1.00[ASN][1000 genomes]
rs41280570	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150400	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4150402	1.00[CHB][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];1.00[ASN][1000 genomes]
rs4150416	1.00[ASN][1000 genomes]
rs4150471	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4150474	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4150499	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4150523	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4536600	0.81[MEX][hapmap]
rs4662713	1.00[ASN][1000 genomes]
rs4662718	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4662719	1.00[ASN][1000 genomes]
rs4662720	0.89[LWK][hapmap];0.81[MKK][hapmap];1.00[ASN][1000 genomes]
rs4662736	1.00[ASN][1000 genomes]
rs55998444	1.00[ASN][1000 genomes]
rs56273408	1.00[ASN][1000 genomes]
rs5937	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59378658	1.00[ASN][1000 genomes]
rs61422716	1.00[ASN][1000 genomes]
rs6430933	1.00[ASN][1000 genomes]
rs6430936	1.00[ASN][1000 genomes]
rs6430938	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733478	1.00[ASN][1000 genomes]
rs6738690	1.00[ASN][1000 genomes]
rs6753288	0.81[MEX][hapmap]
rs6755028	0.81[MEX][hapmap]
rs6756535	1.00[ASN][1000 genomes]
rs72845944	1.00[ASN][1000 genomes]
rs72845975	1.00[ASN][1000 genomes]
rs72845976	1.00[ASN][1000 genomes]
rs72845979	0.80[AFR][1000 genomes]
rs72845982	0.80[AFR][1000 genomes]
rs72845991	1.00[ASN][1000 genomes]
rs72845993	1.00[ASN][1000 genomes]
rs72845997	1.00[ASN][1000 genomes]
rs72846002	1.00[ASN][1000 genomes]
rs72848604	1.00[ASN][1000 genomes]
rs72848612	1.00[ASN][1000 genomes]
rs72848615	1.00[ASN][1000 genomes]
rs72848616	1.00[ASN][1000 genomes]
rs72848618	1.00[ASN][1000 genomes]
rs7556675	1.00[CHB][hapmap];0.86[LWK][hapmap];1.00[ASN][1000 genomes]
rs7562428	1.00[ASN][1000 genomes]
rs7582598	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7590030	0.81[ASW][hapmap];0.86[CEU][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.96[YRI][hapmap]
rs7599210	0.81[MEX][hapmap]
rs7607907	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs777554	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs777569	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9287540	1.00[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	nsv583036	chr2:128173819-128183914	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2069904	ERCC3	cis	parietal	SCAN
rs2069904	ERCC3	cis	cerebellum	SCAN
rs2069904	BIN1	cis	parietal	SCAN
rs2069904	ERCC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128172800-128176800	Weak transcription	NHDF-Ad	bronchial
2	chr2:128174000-128175800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:128174000-128177800	Enhancers	A549	lung
4	chr2:128174000-128180600	Weak transcription	Right Atrium	heart
5	chr2:128174200-128175800	Weak transcription	Gastric	stomach
6	chr2:128174400-128175800	Weak transcription	Pancreas	Pancrea
7	chr2:128174400-128176800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:128174800-128175800	Enhancers	Liver	Liver
9	chr2:128174800-128180400	Weak transcription	Spleen	Spleen
10	chr2:128175000-128177200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:128175000-128180000	Weak transcription	Primary B cells from cord blood	blood
12	chr2:128175200-128176000	Flanking Active TSS	HepG2	liver
13	chr2:128175200-128176200	Enhancers	Dnd41	blood
14	chr2:128175600-128177800	Weak transcription	Fetal Thymus	thymus

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