Variant report

Variant	rs13439439
Chromosome Location	chr8:125283572-125283573
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	NFIC	chr8:125283503-125284200	SK-N-SH	brain:	n/a	n/a
2	JUND	chr8:125283298-125284752	SK-N-SH	brain:	n/a	chr8:125283895-125283905 chr8:125283895-125283905 chr8:125283816-125283826 chr8:125283894-125283906 chr8:125283896-125283904 chr8:125283816-125283826
3	GATA3	chr8:125283502-125284763	SK-N-SH	brain:	n/a	n/a
4	FOSL1	chr8:125283378-125284832	HCT-116	colon:	n/a	chr8:125283895-125283905 chr8:125283894-125283905 chr8:125283895-125283905 chr8:125283816-125283826 chr8:125283894-125283906 chr8:125283896-125283904 chr8:125283816-125283826
5	GTF2F1	chr8:125283387-125284727	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr8:125283333-125284783	Hela-S3	cervix:	n/a	n/a
7	STAT3	chr8:125283396-125284102	MCF10A-Er-Src	breast:	n/a	n/a
8	MAX	chr8:125283061-125284624	A549	lung:	n/a	chr8:125283297-125283308 chr8:125283296-125283311 chr8:125283896-125283905
9	GATA3	chr8:125283373-125285297	A549	lung:	n/a	n/a
10	TEAD4	chr8:125283533-125284794	A549	lung:	n/a	n/a
11	ZBTB33	chr8:125283571-125284093	A549	lung:	n/a	n/a
12	BCL3	chr8:125283453-125284859	A549	lung:	n/a	chr8:125283896-125283905 chr8:125284463-125284472
13	RAD21	chr8:125283463-125284879	A549	lung:	n/a	chr8:125284351-125284361
14	TCF12	chr8:125283565-125284637	A549	lung:	n/a	n/a
15	SP1	chr8:125283387-125284862	HCT-116	colon:	n/a	chr8:125284351-125284365 chr8:125284805-125284812 chr8:125284355-125284364 chr8:125284354-125284366
16	EP300	chr8:125283295-125284932	A549	lung:	n/a	chr8:125284179-125284188
17	SP1	chr8:125283130-125284899	A549	lung:	n/a	chr8:125284351-125284365 chr8:125284805-125284812 chr8:125284355-125284364 chr8:125284354-125284366
18	KAP1	chr8:125283512-125284755	HEK293	kidney:	n/a	n/a
19	RAD21	chr8:125283516-125284760	A549	lung:	n/a	chr8:125284351-125284361
20	JUND	chr8:125283565-125284795	HCT-116	colon:	n/a	chr8:125283895-125283905 chr8:125283895-125283905 chr8:125283816-125283826 chr8:125283894-125283906 chr8:125283896-125283904 chr8:125283816-125283826
21	TCF12	chr8:125281667-125285056	A549	lung:	n/a	n/a
22	MAX	chr8:125283222-125284660	Hela-S3	cervix:	n/a	chr8:125283297-125283308 chr8:125283296-125283311 chr8:125283896-125283905
23	CBX3	chr8:125283507-125284769	HCT-116	colon:	n/a	chr8:125284602-125284613
24	POLR2A	chr8:125283199-125285642	IMR90	lung:	n/a	n/a
25	FOSL2	chr8:125283230-125285044	A549	lung:	n/a	chr8:125283814-125283825 chr8:125283895-125283905 chr8:125283895-125283905 chr8:125283816-125283826 chr8:125283894-125283906 chr8:125283896-125283904 chr8:125283816-125283826
26	PBX3	chr8:125283549-125284179	SK-N-SH	brain:	n/a	n/a
27	EP300	chr8:125283300-125284900	A549	lung:	n/a	chr8:125284179-125284188
28	JUND	chr8:125283451-125284778	HCT-116	colon:	n/a	chr8:125283895-125283905 chr8:125283895-125283905 chr8:125283816-125283826 chr8:125283894-125283906 chr8:125283896-125283904 chr8:125283816-125283826
29	FOSL1	chr8:125283523-125284795	HCT-116	colon:	n/a	chr8:125283895-125283905 chr8:125283894-125283905 chr8:125283895-125283905 chr8:125283816-125283826 chr8:125283894-125283906 chr8:125283896-125283904 chr8:125283816-125283826
30	JUN	chr8:125283562-125284745	Hela-S3	cervix:	n/a	chr8:125283895-125283905 chr8:125283895-125283905 chr8:125283816-125283826 chr8:125283894-125283906 chr8:125283896-125283904 chr8:125283816-125283826
31	FOSL2	chr8:125283562-125284775	SK-N-SH	brain:	n/a	chr8:125283814-125283825 chr8:125283895-125283905 chr8:125283895-125283905 chr8:125283816-125283826 chr8:125283894-125283906 chr8:125283896-125283904 chr8:125283816-125283826
32	SMARCC1	chr8:125282669-125285078	Hela-S3	cervix:	n/a	n/a
33	FOSL2	chr8:125283565-125284127	MCF-7	breast:	n/a	chr8:125283814-125283825 chr8:125283895-125283905 chr8:125283895-125283905 chr8:125283816-125283826 chr8:125283894-125283906 chr8:125283896-125283904 chr8:125283816-125283826
34	SP1	chr8:125283324-125284928	A549	lung:	n/a	chr8:125284351-125284365 chr8:125284805-125284812 chr8:125284355-125284364 chr8:125284354-125284366
35	GATA3	chr8:125283489-125284780	SK-N-SH	brain:	n/a	n/a
36	FOS	chr8:125283384-125284870	MCF10A-Er-Src	breast:	n/a	chr8:125283894-125283905 chr8:125283815-125283826 chr8:125283895-125283905 chr8:125283895-125283905 chr8:125283816-125283826 chr8:125283894-125283906 chr8:125283896-125283904 chr8:125283816-125283826
37	ATF3	chr8:125283486-125284659	A549	lung:	n/a	n/a
38	SP1	chr8:125283440-125284824	HCT-116	colon:	n/a	chr8:125284351-125284365 chr8:125284805-125284812 chr8:125284355-125284364 chr8:125284354-125284366
39	CEBPB	chr8:125283521-125284798	A549	lung:	n/a	n/a
40	KAP1	chr8:125283499-125284717	U2OS	brain:	n/a	n/a
41	CHD2	chr8:125283486-125284712	Hela-S3	cervix:	n/a	chr8:125284354-125284364
42	REST	chr8:125283243-125285045	A549	lung:	n/a	chr8:125284626-125284634
43	RAD21	chr8:125283550-125284514	A549	lung:	n/a	chr8:125284351-125284361
44	ATF3	chr8:125283516-125284814	A549	lung:	n/a	n/a
45	JUND	chr8:125283494-125284771	A549	lung:	n/a	chr8:125283895-125283905 chr8:125283895-125283905 chr8:125283816-125283826 chr8:125283894-125283906 chr8:125283896-125283904 chr8:125283816-125283826
46	SMC3	chr8:125283572-125284962	Hela-S3	cervix:	n/a	n/a
47	ZNF263	chr8:125283557-125284461	HEK293-T-REx	kidney:	n/a	n/a
48	RCOR1	chr8:125283499-125284748	Hela-S3	cervix:	n/a	n/a
49	FOSL2	chr8:125283523-125284685	A549	lung:	n/a	chr8:125283814-125283825 chr8:125283895-125283905 chr8:125283895-125283905 chr8:125283816-125283826 chr8:125283894-125283906 chr8:125283896-125283904 chr8:125283816-125283826
50	BCL3	chr8:125283504-125284780	A549	lung:	n/a	chr8:125283896-125283905 chr8:125284463-125284472

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:125274766..125276637-chr8:125281262..125283690,2	MCF-7	breast:
2	chr8:125283455..125287567-chr8:125381773..125385340,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253227	TF binding region
ENSG00000164983	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10087001	0.81[ASN][1000 genomes]
rs10087062	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10087137	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10087222	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10087374	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10089870	0.89[ASN][1000 genomes]
rs10091808	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10092616	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13439237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13439443	1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs17295226	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17295548	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17360690	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs17360711	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs17360746	1.00[CEU][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17360788	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4360277	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs4374970	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4504618	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4593526	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4871476	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4871477	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4871478	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4871480	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4871481	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4871482	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55784871	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55932688	0.86[ASN][1000 genomes]
rs55945711	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56068026	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56218959	0.83[ASN][1000 genomes]
rs56234976	0.92[ASN][1000 genomes]
rs56383080	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60167901	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60995425	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66467223	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66961607	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67153514	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67712436	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67815046	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68047305	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6983392	0.84[ASN][1000 genomes]
rs6984141	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6984458	0.96[EUR][1000 genomes]
rs6984642	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6984921	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6986310	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6988141	0.85[ASN][1000 genomes]
rs7003238	0.84[ASN][1000 genomes]
rs7003974	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7011052	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7011213	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7011528	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72719397	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73330303	0.92[ASN][1000 genomes]
rs73330304	0.92[ASN][1000 genomes]
rs73345158	0.81[ASN][1000 genomes]
rs73345172	0.85[ASN][1000 genomes]
rs73345176	0.84[ASN][1000 genomes]
rs73345185	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7842882	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9297691	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs9297693	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9643192	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9969472	1.00[CEU][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9969473	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9969475	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9969479	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9969480	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9969624	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[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	esv2762769	chr8:125167256-125480574	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13439439	RP11-383J24.1	cis	Muscle Skeletal	GTEx
rs13439439	TRMT12	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125274800-125287400	Weak transcription	Fetal Brain Male	brain
2	chr8:125279400-125284000	Weak transcription	Right Ventricle	heart
3	chr8:125280400-125284000	Weak transcription	Pancreas	Pancrea
4	chr8:125280400-125284000	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr8:125281000-125283600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr8:125281200-125284400	Enhancers	Fetal Intestine Large	intestine
7	chr8:125281200-125284600	Enhancers	Psoas Muscle	Psoas
8	chr8:125281600-125283600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr8:125281600-125284000	Enhancers	K562	blood
10	chr8:125281600-125284200	Weak transcription	Right Atrium	heart
11	chr8:125281600-125285000	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr8:125281800-125283800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr8:125282000-125284000	Weak transcription	Fetal Heart	heart
14	chr8:125282000-125284200	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr8:125282200-125283600	Flanking Active TSS	A549	lung
16	chr8:125282200-125283600	Enhancers	Osteobl	bone
17	chr8:125282200-125284000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr8:125282200-125284400	Enhancers	Fetal Intestine Small	intestine
19	chr8:125282200-125285600	Enhancers	NHDF-Ad	bronchial
20	chr8:125282400-125284000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr8:125282400-125284600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr8:125282600-125284600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr8:125282800-125284400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr8:125282800-125284400	Enhancers	Left Ventricle	heart
25	chr8:125282800-125284400	Enhancers	HSMMtube	muscle
26	chr8:125282800-125284800	Enhancers	HUVEC	blood vessel
27	chr8:125282800-125285400	Flanking Active TSS	Hela-S3	cervix
28	chr8:125282800-125285400	Enhancers	NHLF	lung
29	chr8:125282800-125285600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr8:125283200-125283600	Enhancers	Rectal Smooth Muscle	rectum
31	chr8:125283200-125284000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr8:125283200-125284400	Enhancers	Colon Smooth Muscle	Colon
33	chr8:125283200-125285000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr8:125283200-125285600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr8:125283400-125283600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr8:125283400-125283600	Enhancers	Colonic Mucosa	Colon
37	chr8:125283400-125283600	Flanking Active TSS	NH-A	brain
38	chr8:125283400-125283800	Enhancers	Stomach Smooth Muscle	stomach
39	chr8:125283400-125284400	Enhancers	HMEC	breast
40	chr8:125283400-125284400	Enhancers	NHEK	skin
41	chr8:125283400-125284600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr8:125283400-125284600	Enhancers	HSMM	muscle
43	chr8:125283400-125285400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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