Variant report

Variant	rs12499248
Chromosome Location	chr4:103277284-103277285
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	CEBPD	chr4:103276781-103277457	K562	blood:	n/a	n/a
2	ATF1	chr4:103277011-103277515	K562	blood:	n/a	n/a
3	PML	chr4:103276720-103277473	K562	blood:	n/a	chr4:103277031-103277039
4	MXI1	chr4:103276893-103277581	K562	blood:	n/a	n/a
5	GABPA	chr4:103276822-103277326	K562	blood:	n/a	n/a
6	GATA2	chr4:103276878-103277306	K562	blood:	n/a	n/a
7	TBL1XR1	chr4:103276890-103277581	K562	blood:	n/a	n/a
8	TEAD4	chr4:103276683-103277692	K562	blood:	n/a	n/a
9	ZNF274	chr4:103276677-103277495	K562	blood:	n/a	n/a
10	GATA2	chr4:103276717-103277673	K562	blood:	n/a	chr4:103277451-103277460
11	JUND	chr4:103277271-103277511	HepG2	liver:	n/a	n/a
12	TAL1	chr4:103276794-103277719	K562	blood:	n/a	chr4:103277515-103277530 chr4:103277518-103277529 chr4:103277515-103277530 chr4:103277515-103277530 chr4:103277453-103277461
13	STAT5A	chr4:103276808-103277584	K562	blood:	n/a	n/a
14	ZNF384	chr4:103277058-103277376	K562	blood:	n/a	n/a
15	CREB1	chr4:103276746-103277578	K562	blood:	n/a	n/a
16	GATA1	chr4:103276807-103277693	K562	blood:	n/a	chr4:103277451-103277460
17	TEAD4	chr4:103276740-103277715	K562	blood:	n/a	n/a
18	GATA2	chr4:103276781-103277343	K562	blood:	n/a	n/a
19	ZMIZ1	chr4:103276872-103277544	K562	blood:	n/a	n/a
20	NR2F2	chr4:103276714-103277651	K562	blood:	n/a	n/a
21	NR2F2	chr4:103276825-103277339	K562	blood:	n/a	n/a
22	JUND	chr4:103276949-103277285	K562	blood:	n/a	n/a
23	STAT5A	chr4:103276811-103277307	K562	blood:	n/a	n/a
24	ARID3A	chr4:103276841-103277620	K562	blood:	n/a	n/a
25	EP300	chr4:103276828-103277629	K562	blood:	n/a	n/a
26	TRIM28	chr4:103276841-103277426	K562	blood:	n/a	chr4:103277031-103277039
27	CEBPB	chr4:103277007-103277440	K562	blood:	n/a	n/a
28	IRF1	chr4:103276956-103277534	K562	blood:	n/a	chr4:103276978-103276992 chr4:103276982-103276993
29	CEBPD	chr4:103276847-103277705	K562	blood:	n/a	n/a
30	PML	chr4:103276779-103277376	K562	blood:	n/a	chr4:103277031-103277039

No.	Distal block	Cell Line	Cell type
1	chr4:103275483..103277886-chr4:103279465..103281721,2	K562	blood:
2	chr4:103265430..103268182-chr4:103276336..103278221,2	MCF-7	breast:
3	chr4:103264370..103266678-chr4:103275427..103278111,3	K562	blood:

Variant related genes	Relation type
SLC39A8	TF binding region
ENSG00000138821	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10019247	0.83[EUR][1000 genomes]
rs10461136	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11097776	0.93[EUR][1000 genomes]
rs11097780	0.84[EUR][1000 genomes]
rs1117520	1.00[CEU][hapmap]
rs1117522	0.95[EUR][1000 genomes]
rs1159788	0.95[EUR][1000 genomes]
rs11728286	0.95[EUR][1000 genomes]
rs11730379	0.96[EUR][1000 genomes]
rs11730944	0.91[EUR][1000 genomes]
rs11730958	0.94[EUR][1000 genomes]
rs11931217	0.87[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs11935847	0.93[EUR][1000 genomes]
rs12500141	0.83[EUR][1000 genomes]
rs12505568	0.83[EUR][1000 genomes]
rs12510124	0.91[CEU][hapmap];0.92[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs13104988	0.83[EUR][1000 genomes]
rs13107285	0.95[EUR][1000 genomes]
rs13112930	0.88[EUR][1000 genomes]
rs13114804	0.84[EUR][1000 genomes]
rs13125848	0.93[EUR][1000 genomes]
rs13147260	0.87[EUR][1000 genomes]
rs1381893	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1381894	0.88[EUR][1000 genomes]
rs1381895	0.88[EUR][1000 genomes]
rs1381897	0.87[EUR][1000 genomes]
rs1381899	0.95[EUR][1000 genomes]
rs1462943	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1462948	0.95[EUR][1000 genomes]
rs1462949	0.94[EUR][1000 genomes]
rs1462950	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs1462951	0.95[EUR][1000 genomes]
rs1462952	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs1599684	0.95[EUR][1000 genomes]
rs1599685	0.95[EUR][1000 genomes]
rs1599686	0.84[EUR][1000 genomes]
rs1870952	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs2054393	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2086004	0.95[EUR][1000 genomes]
rs2126625	0.96[EUR][1000 genomes]
rs233820	0.81[JPT][hapmap]
rs34663993	0.83[ASN][1000 genomes]
rs34835832	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4557261	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4699012	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699019	0.94[EUR][1000 genomes]
rs4699021	0.94[EUR][1000 genomes]
rs4699024	0.93[EUR][1000 genomes]
rs4699026	0.86[CEU][hapmap];0.90[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs56202729	0.85[ASN][1000 genomes]
rs62329487	0.85[ASN][1000 genomes]
rs6533014	0.83[GIH][hapmap]
rs6810692	0.81[EUR][1000 genomes]
rs6814302	0.95[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs6835467	0.93[EUR][1000 genomes]
rs6843751	0.94[EUR][1000 genomes]
rs6844796	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6848517	0.82[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap]
rs7436937	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7657947	0.93[EUR][1000 genomes]
rs7661593	0.95[EUR][1000 genomes]
rs7683109	0.94[EUR][1000 genomes]
rs962399	0.95[EUR][1000 genomes]
rs984055	0.93[EUR][1000 genomes]
rs985989	0.94[CHB][hapmap];0.86[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12499248	GSTCD	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103272600-103284200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:103274200-103283400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:103274800-103278800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr4:103275200-103284400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:103275800-103278400	Enhancers	Liver	Liver
6	chr4:103276600-103278000	Weak transcription	Fetal Intestine Large	intestine
7	chr4:103277000-103278000	Enhancers	K562	blood
8	chr4:103277200-103284600	Weak transcription	Rectal Mucosa Donor 29	rectum

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