Variant report

Variant	rs4124874
Chromosome Location	chr2:234665659-234665660
allele	A/C
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	EP300	chr2:234665382-234665803	HepG2	liver:	n/a	n/a
2	USF1	chr2:234665180-234665761	A549	lung:	n/a	n/a
3	TCF12	chr2:234665288-234665854	HepG2	liver:	n/a	n/a
4	JUND	chr2:234665186-234665923	A549	lung:	n/a	n/a
5	ELF1	chr2:234665363-234665770	HepG2	liver:	n/a	n/a
6	REST	chr2:234665294-234665976	HepG2	liver:	n/a	chr2:234665856-234665876 chr2:234665735-234665748 chr2:234665856-234665876 chr2:234665856-234665869
7	HNF4A	chr2:234665337-234665848	HepG2	liver:	n/a	chr2:234665643-234665656 chr2:234665643-234665656 chr2:234665591-234665606 chr2:234665642-234665657 chr2:234665639-234665661
8	REST	chr2:234665262-234665719	A549	lung:	n/a	n/a
9	USF1	chr2:234665253-234665810	A549	lung:	n/a	n/a
10	NR3C1	chr2:234665053-234665990	A549	lung:	n/a	n/a
11	GABPA	chr2:234665175-234665784	A549	lung:	n/a	n/a
12	NR2F2	chr2:234665223-234666023	HepG2	liver:	n/a	chr2:234665444-234665459
13	RFX5	chr2:234665463-234665739	HepG2	liver:	n/a	n/a
14	FOXA2	chr2:234665158-234665999	A549	lung:	n/a	n/a
15	EP300	chr2:234664946-234666071	A549	lung:	n/a	chr2:234665216-234665225
16	JUND	chr2:234665389-234665779	HepG2	liver:	n/a	n/a
17	ZBTB33	chr2:234665352-234665729	HepG2	liver:	n/a	n/a
18	ELF1	chr2:234665287-234665705	A549	lung:	n/a	n/a
19	REST	chr2:234665180-234666038	A549	lung:	n/a	chr2:234665856-234665876 chr2:234665735-234665748 chr2:234665856-234665876 chr2:234665856-234665869
20	SIX5	chr2:234665293-234665787	A549	lung:	n/a	n/a
21	CEBPB	chr2:234665269-234665761	A549	lung:	n/a	chr2:234665476-234665488 chr2:234665429-234665440
22	FOSL2	chr2:234665355-234665937	HepG2	liver:	n/a	n/a
23	CEBPB	chr2:234665245-234665826	HepG2	liver:	n/a	chr2:234665476-234665488 chr2:234665429-234665440
24	MBD4	chr2:234665232-234665857	HepG2	liver:	n/a	n/a
25	EP300	chr2:234665228-234665863	HepG2	liver:	n/a	n/a
26	CREB1	chr2:234665410-234665788	A549	lung:	n/a	n/a
27	MAZ	chr2:234665427-234665787	HepG2	liver:	n/a	chr2:234665738-234665748
28	GATA3	chr2:234665206-234665942	A549	lung:	n/a	n/a
29	EP300	chr2:234665041-234665982	A549	lung:	n/a	chr2:234665216-234665225
30	JUND	chr2:234665436-234665829	HepG2	liver:	n/a	n/a
31	CEBPB	chr2:234665312-234665783	A549	lung:	n/a	chr2:234665476-234665488 chr2:234665429-234665440
32	HDAC2	chr2:234665224-234665850	HepG2	liver:	n/a	n/a
33	MYBL2	chr2:234664829-234665981	HepG2	liver:	n/a	n/a
34	TEAD4	chr2:234665385-234665734	HepG2	liver:	n/a	n/a
35	MAX	chr2:234665223-234665952	A549	lung:	n/a	chr2:234665738-234665748
36	CEBPD	chr2:234665334-234665685	HepG2	liver:	n/a	n/a
37	FOXA1	chr2:234664847-234665924	HepG2	liver:	n/a	n/a
38	JUND	chr2:234665279-234665940	A549	lung:	n/a	n/a
39	CEBPB	chr2:234665343-234665750	HepG2	liver:	n/a	chr2:234665476-234665488 chr2:234665429-234665440
40	FOXA1	chr2:234665199-234665867	HepG2	liver:	n/a	n/a
41	FOSL2	chr2:234665168-234665967	A549	lung:	n/a	n/a
42	TAF1	chr2:234665259-234665803	A549	lung:	n/a	n/a
43	MBD4	chr2:234665166-234665864	HepG2	liver:	n/a	n/a
44	ZBTB33	chr2:234665241-234665748	A549	lung:	n/a	n/a
45	FOSL2	chr2:234665356-234665899	HepG2	liver:	n/a	n/a
46	CEBPB	chr2:234665270-234665777	HepG2	liver:	n/a	chr2:234665476-234665488 chr2:234665429-234665440
47	FOSL2	chr2:234665276-234665787	A549	lung:	n/a	n/a
48	BHLHE40	chr2:234665457-234665720	HepG2	liver:	n/a	n/a
49	ZBTB33	chr2:234665480-234665745	HepG2	liver:	n/a	n/a
50	RXRA	chr2:234665224-234665838	HepG2	liver:	n/a	chr2:234665447-234665456

Variant related genes	Relation type
UGT1A1	TF binding region
UGT1A8	TF binding region
ENSG00000178836	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10179091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10929301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1104892	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11685892	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17862866	0.85[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2008595	0.85[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2221198	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2363116	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3755319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806596	0.92[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3806597	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs3821242	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4148326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4294999	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4399719	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4467260	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4521035	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4663333	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4663963	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4663965	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4663967	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4663969	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4663971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6431628	0.85[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6706232	0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6711351	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6715325	0.92[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6741669	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6760025	1.00[YRI][hapmap]
rs7556676	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7572563	0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7574296	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs759174	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7597496	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs871514	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv3215	chr2:234631123-234670276	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv1811811	chr2:234633964-234709430	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	esv1808921	chr2:234648954-234666236	Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv1811500	chr2:234648954-234666236	Bivalent Enhancer Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv876018	chr2:234653938-234666461	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4124874	DGKD	cis	cerebellum	SCAN
rs4124874	SH3BP4	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234626600-234668400	Weak transcription	NHEK	skin
2	chr2:234646400-234666600	Weak transcription	Stomach Mucosa	stomach
3	chr2:234660000-234666200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:234660200-234666400	Weak transcription	Colonic Mucosa	Colon
5	chr2:234664000-234666400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:234664000-234669000	Weak transcription	Esophagus	oesophagus
7	chr2:234664000-234669200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:234664200-234668800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:234664200-234669000	Enhancers	Liver	Liver
10	chr2:234664800-234666400	Enhancers	HepG2	liver
11	chr2:234664800-234671000	Enhancers	Fetal Intestine Small	intestine
12	chr2:234665200-234669200	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr2:234665600-234665800	Flanking Active TSS	A549	lung
14	chr2:234665600-234667000	Weak transcription	Osteobl	bone
15	chr2:234665600-234670800	Enhancers	Fetal Intestine Large	intestine

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