Variant report

Variant	rs7572563
Chromosome Location	chr2:234617236-234617237
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	FOSL2	chr2:234616319-234617392	A549	lung:	n/a	n/a
2	MAX	chr2:234616100-234618160	A549	lung:	n/a	n/a
3	ATF3	chr2:234616457-234617245	A549	lung:	n/a	n/a
4	GATA3	chr2:234616484-234617384	A549	lung:	n/a	chr2:234617062-234617078 chr2:234617067-234617074 chr2:234617065-234617075 chr2:234617067-234617074 chr2:234617066-234617074 chr2:234617067-234617074 chr2:234617067-234617077
5	JUND	chr2:234616570-234617322	A549	lung:	n/a	n/a
6	POLR2A	chr2:234617090-234617384	A549	lung:	n/a	n/a
7	GATA3	chr2:234616280-234617649	A549	lung:	n/a	chr2:234617062-234617078 chr2:234617067-234617074 chr2:234617065-234617075 chr2:234617067-234617074 chr2:234617066-234617074 chr2:234617067-234617074 chr2:234617067-234617077
8	CEBPB	chr2:234616573-234617381	A549	lung:	n/a	n/a
9	CEBPB	chr2:234616408-234617617	A549	lung:	n/a	n/a
10	SP1	chr2:234616293-234617482	A549	lung:	n/a	chr2:234617399-234617413 chr2:234617400-234617409 chr2:234617404-234617413
11	CEBPB	chr2:234616597-234617345	Hela-S3	cervix:	n/a	n/a
12	FOXA2	chr2:234616982-234617483	A549	lung:	n/a	n/a
13	BCL3	chr2:234616263-234617452	A549	lung:	n/a	n/a
14	EP300	chr2:234616111-234617875	A549	lung:	n/a	n/a
15	E2F6	chr2:234616344-234617452	A549	lung:	n/a	n/a
16	SIN3AK20	chr2:234616592-234617287	A549	lung:	n/a	n/a
17	RAD21	chr2:234616452-234617270	A549	lung:	n/a	n/a
18	FOXA2	chr2:234616476-234617424	A549	lung:	n/a	n/a
19	USF1	chr2:234616400-234617287	A549	lung:	n/a	n/a
20	EP300	chr2:234616109-234617400	A549	lung:	n/a	n/a
21	ETS1	chr2:234616511-234617287	A549	lung:	n/a	n/a
22	TCF12	chr2:234615996-234618019	A549	lung:	n/a	n/a
23	SP1	chr2:234616247-234617981	A549	lung:	n/a	chr2:234617399-234617413 chr2:234617400-234617409 chr2:234617404-234617413
24	SIN3AK20	chr2:234616494-234617307	A549	lung:	n/a	n/a
25	SIX5	chr2:234616607-234617944	A549	lung:	n/a	n/a
26	POLR2A	chr2:234617058-234617349	A549	lung:	n/a	n/a
27	TCF12	chr2:234616575-234617298	A549	lung:	n/a	n/a
28	MAX	chr2:234616171-234617419	A549	lung:	n/a	n/a
29	CEBPB	chr2:234616376-234617413	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234616675..234619386-chr2:234621500..234623443,3	MCF-7	breast:
2	chr2:234400105..234405009-chr2:234616033..234619892,4	MCF-7	breast:
3	chr2:234386983..234399433-chr2:234613282..234621553,23	MCF-7	breast:
4	chr2:234597435..234606028-chr2:234613419..234620116,22	MCF-7	breast:
5	chr2:234599124..234606471-chr2:234613478..234621007,17	MCF-7	breast:
6	chr2:234393460..234398388-chr2:234612624..234620814,16	MCF-7	breast:
7	chr2:234388450..234390817-chr2:234616855..234619470,2	MCF-7	breast:

Variant related genes	Relation type
UGT1A5	TF binding region
UGT1A8	TF binding region
ENSG00000240224	Chromatin interaction
ENSG00000167165	Chromatin interaction
ENSG00000085982	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10179091	0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs10929301	0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1104892	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685892	0.86[ASN][1000 genomes]
rs17862866	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2008595	0.93[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs2012734	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2221198	0.82[CHB][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs2363116	0.87[ASN][1000 genomes]
rs3755319	0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs3806596	0.85[CEU][hapmap];0.93[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3806597	0.85[CEU][hapmap];0.93[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap]
rs3821242	0.82[ASN][1000 genomes]
rs4124874	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]
rs4148326	0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs4233633	0.86[CHB][hapmap]
rs4294999	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs4399719	0.93[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4467260	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4521035	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4663325	0.86[CHB][hapmap]
rs4663327	0.86[CHB][hapmap]
rs4663333	0.93[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4663963	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs4663965	0.85[CEU][hapmap];0.93[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs4663967	0.93[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4663969	0.82[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs4663971	0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs6431628	0.93[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6706232	0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6711351	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6715325	0.93[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[ASN][1000 genomes]
rs6741669	0.85[CEU][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6760025	1.00[YRI][hapmap]
rs7556676	0.82[CHB][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs7574296	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7597496	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs871514	0.85[CEU][hapmap];0.93[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	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
5	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
6	esv2760615	chr2:234613030-234640233	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7572563	DGKD	cis	cerebellum	SCAN
rs7572563	ARL4C	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234614000-234617400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:234614400-234618000	Enhancers	Stomach Mucosa	stomach
3	chr2:234614800-234617400	Enhancers	Osteobl	bone
4	chr2:234614800-234617800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:234615000-234617400	Enhancers	NH-A	brain
6	chr2:234615000-234619800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:234615400-234620400	Weak transcription	Pancreas	Pancrea
8	chr2:234615600-234620000	Weak transcription	Fetal Intestine Large	intestine
9	chr2:234616000-234617400	Flanking Active TSS	A549	lung
10	chr2:234616000-234618600	Weak transcription	Liver	Liver
11	chr2:234616200-234617400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:234617000-234617400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:234617000-234619800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:234617200-234617400	Flanking Active TSS	Hela-S3	cervix
15	chr2:234617200-234617800	Enhancers	Esophagus	oesophagus
16	chr2:234617200-234617800	Enhancers	Gastric	stomach
17	chr2:234617200-234619000	Weak transcription	NHEK	skin

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