Variant report

Variant	rs4760619
Chromosome Location	chr12:48499931-48499932
allele	A/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	TAF1	chr12:48499452-48500440	PFSK-1	brain:	n/a	n/a
2	RELA	chr12:48498987-48500647	GM19099	blood:	n/a	chr12:48499466-48499475 chr12:48499466-48499475
3	MAX	chr12:48499297-48500487	ECC-1	luminal epithelium:	n/a	chr12:48499796-48499806 chr12:48499930-48499940 chr12:48500194-48500203
4	SRF	chr12:48499535-48500442	MCF-7	breast:	n/a	chr12:48499685-48499695
5	TAF1	chr12:48499673-48500307	PFSK-1	brain:	n/a	n/a
6	CTCF	chr12:48499920-48500070	HCT-116	colon:	n/a	n/a
7	E2F4	chr12:48499096-48500197	Hela-S3	cervix:	n/a	chr12:48499791-48499802 chr12:48499462-48499470 chr12:48499463-48499470 chr12:48499382-48499394 chr12:48499662-48499671 chr12:48499459-48499471 chr12:48499792-48499804 chr12:48499679-48499686 chr12:48499981-48499990 chr12:48499463-48499470 chr12:48499978-48499988 chr12:48499463-48499470
8	SIN3AK20	chr12:48499335-48500594	MCF-7	breast:	n/a	n/a
9	SIX5	chr12:48499900-48500230	GM12878	blood:	n/a	n/a
10	CTCF	chr12:48499840-48499990	AG09319	gingival:	n/a	n/a
11	YY1	chr12:48499309-48500356	ECC-1	luminal epithelium:	n/a	chr12:48499662-48499671 chr12:48499779-48499790 chr12:48499719-48499733 chr12:48499641-48499652
12	MAX	chr12:48499369-48500437	A549	lung:	n/a	chr12:48499796-48499806 chr12:48499930-48499940 chr12:48500194-48500203
13	MAX	chr12:48499372-48500340	HepG2	liver:	n/a	chr12:48499796-48499806 chr12:48499930-48499940 chr12:48500194-48500203
14	POLR2A	chr12:48499007-48500318	GM12878	blood:	n/a	n/a
15	GTF2F1	chr12:48499839-48500328	K562	blood:	n/a	n/a
16	POLR2A	chr12:48499022-48500297	K562	blood:	n/a	n/a
17	FOXM1	chr12:48499547-48500445	MCF-7	breast:	n/a	n/a
18	YY1	chr12:48499703-48500273	A549	lung:	n/a	chr12:48499779-48499790 chr12:48499719-48499733
19	REST	chr12:48499192-48500488	A549	lung:	n/a	chr12:48499996-48500016 chr12:48500122-48500140
20	HEY1	chr12:48499358-48500188	K562	blood:	n/a	chr12:48499612-48499627
21	CTCF	chr12:48499880-48500030	Caco-2	colon:	n/a	n/a
22	CTCF	chr12:48499920-48500070	GM06990	blood:	n/a	n/a
23	STAT1	chr12:48499228-48500587	GM12878	blood:	n/a	chr12:48499664-48499676 chr12:48499777-48499789 chr12:48499643-48499655 chr12:48500568-48500576
24	TAF1	chr12:48499107-48500695	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr12:48499641-48500222	HepG2	liver:	n/a	n/a
26	E2F6	chr12:48499662-48499940	K562	blood:	n/a	chr12:48499662-48499671 chr12:48499792-48499804 chr12:48499679-48499686
27	KAP1	chr12:48499790-48500394	U2OS	brain:	n/a	n/a
28	JUND	chr12:48499637-48500324	A549	lung:	n/a	n/a
29	MAX	chr12:48499398-48500308	K562	blood:	n/a	chr12:48499796-48499806 chr12:48499930-48499940 chr12:48500194-48500203
30	UBTF	chr12:48499046-48500421	K562	blood:	n/a	n/a
31	CTCF	chr12:48499860-48500010	AoAF	blood vessel:	n/a	n/a
32	REST	chr12:48499649-48500345	PANC-1	pancreas:	n/a	chr12:48499996-48500016 chr12:48500122-48500140
33	SMC3	chr12:48499804-48500240	K562	blood:	n/a	n/a
34	MAZ	chr12:48499105-48500881	IMR90	lung:	n/a	chr12:48499796-48499806 chr12:48499930-48499940 chr12:48500194-48500203
35	ELF1	chr12:48499557-48500273	HepG2	liver:	n/a	chr12:48499900-48499913 chr12:48499705-48499714 chr12:48499610-48499622
36	ELK1	chr12:48499663-48500344	K562	blood:	n/a	n/a
37	CTCF	chr12:48499872-48499943	GM12891	blood:	n/a	n/a
38	EBF1	chr12:48499047-48500357	GM12878	blood:	n/a	chr12:48499440-48499449 chr12:48499439-48499449
39	SIN3A	chr12:48499325-48500609	GM12878	blood:	n/a	chr12:48499729-48499740
40	CTCF	chr12:48499880-48500030	NHEK	skin:	n/a	n/a
41	POLR2A	chr12:48498887-48501339	GM12878	blood:	n/a	n/a
42	POLR2A	chr12:48499439-48500045	A549	lung:	n/a	n/a
43	BCLAF1	chr12:48499598-48500354	K562	blood:	n/a	chr12:48499816-48499829
44	POU2F2	chr12:48499550-48500375	GM12891	blood:	n/a	chr12:48499637-48499649
45	POLR2A	chr12:48499393-48500272	NB4	blood:	n/a	n/a
46	POLR2A	chr12:48499058-48500406	K562	blood:	n/a	n/a
47	POLR2A	chr12:48498983-48500410	GM15510	blood:	n/a	n/a
48	RUNX3	chr12:48498963-48500459	GM12878	blood:	n/a	n/a
49	GATA3	chr12:48499524-48500449	MCF-7	breast:	n/a	chr12:48500254-48500262 chr12:48500252-48500264
50	POLR2A	chr12:48499827-48500097	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48499595..48500104-chr19:47616435..47617215,2	Hela-S3	cervix:
2	chr12:48492914..48496557-chr12:48498180..48501677,4	MCF-7	breast:
3	chr12:48496939..48501728-chr12:48549612..48553634,6	MCF-7	breast:
4	chr12:48498567..48501846-chr12:48512929..48518601,8	MCF-7	breast:
5	chr12:48499172..48500140-chr22:38712414..38713387,2	Hela-S3	cervix:
6	chr12:48490196..48492740-chr12:48498056..48500665,3	MCF-7	breast:
7	chr1:182758456..182759367-chr12:48499093..48499942,2	Hela-S3	cervix:
8	chr12:48497586..48502171-chr12:48511099..48514258,8	MCF-7	breast:
9	chr12:48499494..48502600-chr12:48549917..48552067,4	MCF-7	breast:
10	chr12:48296929..48299891-chr12:48498540..48500341,2	MCF-7	breast:
11	chr12:48495831..48503326-chr12:48548997..48555180,8	K562	blood:
12	chr12:48497262..48501671-chr12:48511273..48513832,5	K562	blood:
13	chr12:48496389..48500489-chr12:48511491..48515053,4	K562	blood:
14	chr10:101190598..101191541-chr12:48499592..48500567,2	Hela-S3	cervix:

Variant related genes	Relation type
SENP1	TF binding region
PFKM	TF binding region
ENSG00000213923	Chromatin interaction
ENSG00000135838	Chromatin interaction
ENSG00000130749	Chromatin interaction
ENSG00000079387	Chromatin interaction
ENSG00000258051	Chromatin interaction
ENSG00000142230	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000224934	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10082861	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10219623	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10219645	0.82[ASN][1000 genomes]
rs10467101	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs10875724	0.93[JPT][hapmap]
rs10875725	1.00[JPT][hapmap]
rs10875732	1.00[JPT][hapmap]
rs10875745	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10875746	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10875747	0.93[ASN][1000 genomes]
rs10875748	0.93[ASN][1000 genomes]
rs10875750	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10875756	0.86[ASN][1000 genomes]
rs10875767	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs10875770	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs10875772	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs10875792	0.85[JPT][hapmap]
rs10875793	0.80[CHB][hapmap];0.92[JPT][hapmap]
rs11168357	0.93[JPT][hapmap]
rs11168369	1.00[JPT][hapmap]
rs11168371	1.00[JPT][hapmap]
rs11168403	1.00[JPT][hapmap]
rs11168413	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11168414	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11168415	0.90[ASN][1000 genomes]
rs11168416	0.90[ASN][1000 genomes]
rs11168418	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11168420	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11168421	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11168422	0.93[ASN][1000 genomes]
rs11168425	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11168427	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168433	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11168450	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11168459	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12297470	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12301339	0.88[CEU][hapmap]
rs12304476	1.00[JPT][hapmap]
rs12305182	0.93[JPT][hapmap]
rs12305511	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs12306290	0.87[ASN][1000 genomes]
rs12306451	1.00[JPT][hapmap]
rs12310813	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12312134	0.88[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs17122666	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17122812	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs1859445	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2012773	1.00[JPT][hapmap]
rs2079295	0.93[JPT][hapmap]
rs2107638	0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2228500	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2269933	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2269935	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2269936	1.00[JPT][hapmap]
rs2279464	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs2286021	0.91[ASN][1000 genomes]
rs3782910	1.00[JPT][hapmap]
rs4760609	0.93[JPT][hapmap]
rs4760622	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4760681	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4760684	0.90[ASN][1000 genomes]
rs4760687	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4760689	0.86[ASN][1000 genomes]
rs4760690	0.86[ASN][1000 genomes]
rs4760695	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4760696	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4760697	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs60106007	0.90[ASN][1000 genomes]
rs61343568	0.84[ASN][1000 genomes]
rs6580659	1.00[JPT][hapmap]
rs7135779	1.00[JPT][hapmap]
rs719008	0.93[JPT][hapmap]
rs725454	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7299135	0.93[JPT][hapmap]
rs7299271	0.93[JPT][hapmap]
rs7485355	0.91[ASN][1000 genomes]
rs7486424	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs8804	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs886588	1.00[JPT][hapmap]
rs9634261	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs989144	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4760619	SENP1,PFKM	cis	brain	BrainEAC
rs4760619	RP1-228P16.1	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48496600-48500400	Active TSS	GM12878-XiMat	blood
2	chr12:48498200-48500400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:48498200-48500400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:48498200-48500400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr12:48498200-48500400	Active TSS	NHDF-Ad	bronchial
6	chr12:48498200-48500600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:48498200-48500600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:48498400-48500400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:48498400-48500400	Active TSS	Colonic Mucosa	Colon
10	chr12:48498400-48500400	Active TSS	HSMMtube	muscle
11	chr12:48498400-48500600	Active TSS	Fetal Muscle Trunk	muscle
12	chr12:48498600-48500200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:48498600-48500200	Active TSS	Fetal Muscle Leg	muscle
14	chr12:48498600-48500400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:48498600-48500400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:48498600-48500400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr12:48498600-48500400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:48498600-48500400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:48498600-48500400	Active TSS	Fetal Thymus	thymus
20	chr12:48498600-48500400	Active TSS	Lung	lung
21	chr12:48498600-48500400	Active TSS	Psoas Muscle	Psoas
22	chr12:48498600-48500400	Active TSS	Right Ventricle	heart
23	chr12:48498600-48500400	Active TSS	K562	blood
24	chr12:48498600-48500600	Active TSS	H1 Cell Line	embryonic stem cell
25	chr12:48498600-48500600	Active TSS	Left Ventricle	heart
26	chr12:48498800-48500200	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr12:48498800-48500200	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr12:48498800-48500200	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr12:48498800-48500200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:48498800-48500400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:48498800-48500400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:48498800-48500400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:48498800-48500400	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr12:48498800-48500400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:48498800-48500400	Active TSS	Primary T cells fromperipheralblood	blood
36	chr12:48498800-48500400	Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr12:48498800-48500400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:48498800-48500400	Active TSS	Fetal Intestine Large	intestine
39	chr12:48498800-48500400	Active TSS	Fetal Intestine Small	intestine
40	chr12:48498800-48500400	Active TSS	Fetal Stomach	stomach
41	chr12:48498800-48500400	Active TSS	A549	lung
42	chr12:48498800-48500400	Active TSS	HMEC	breast
43	chr12:48498800-48500400	Active TSS	HSMM	muscle
44	chr12:48498800-48500400	Active TSS	NHLF	lung
45	chr12:48498800-48500600	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr12:48498800-48500600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:48498800-48500600	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr12:48499000-48500200	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr12:48499000-48500200	Active TSS	Stomach Mucosa	stomach
50	chr12:48499000-48500200	Active TSS	Hela-S3	cervix

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