Variant report

Variant	rs3754907
Chromosome Location	chr2:20251758-20251759
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	PBX3	chr2:20251044-20252225	A549	lung:	n/a	chr2:20251483-20251492
2	YY1	chr2:20251021-20252049	K562	blood:	n/a	chr2:20251849-20251858 chr2:20251846-20251860
3	RCOR1	chr2:20251504-20252097	K562	blood:	n/a	n/a
4	POLR2A	chr2:20251145-20252201	HUVEC	blood vessel:	n/a	n/a
5	NR2F2	chr2:20251455-20251973	K562	blood:	n/a	chr2:20251810-20251825
6	YY1	chr2:20251126-20252395	SK-N-SH	brain:	n/a	chr2:20251849-20251858 chr2:20251846-20251860
7	SP1	chr2:20251147-20252051	GM12878	blood:	n/a	chr2:20251845-20251859 chr2:20251849-20251859 chr2:20251481-20251502 chr2:20251848-20251860 chr2:20251850-20251859 chr2:20251849-20251859 chr2:20251848-20251860 chr2:20251850-20251859 chr2:20251391-20251401 chr2:20251849-20251858
8	CEBPB	chr2:20251554-20252136	MCF-7	breast:	n/a	n/a
9	POLR2A	chr2:20251041-20252121	HL-60	blood:	n/a	n/a
10	POLR2A	chr2:20251056-20252093	GM12891	blood:	n/a	n/a
11	CEBPB	chr2:20251336-20252051	HepG2	liver:	n/a	n/a
12	TAF1	chr2:20250346-20252400	H1-hESC	embryonic stem cell:	n/a	n/a
13	CHD2	chr2:20251151-20252072	Hela-S3	cervix:	n/a	n/a
14	MAX	chr2:20251080-20252413	SK-N-SH	brain:	n/a	n/a
15	NFYA	chr2:20251190-20252076	Hela-S3	cervix:	n/a	chr2:20251513-20251531
16	POLR2A	chr2:20251120-20252378	HepG2	liver:	n/a	n/a
17	NRF1	chr2:20251258-20252025	K562	blood:	n/a	chr2:20251849-20251858 chr2:20251426-20251437 chr2:20251428-20251437 chr2:20251426-20251437 chr2:20251423-20251437 chr2:20251426-20251440
18	POLR2A	chr2:20251097-20252132	GM18505	blood:	n/a	n/a
19	STAT1	chr2:20251163-20252033	GM12878	blood:	n/a	n/a
20	ELF1	chr2:20251684-20251957	K562	blood:	n/a	n/a
21	BHLHE40	chr2:20251197-20252116	A549	lung:	n/a	chr2:20251401-20251417
22	ELK1	chr2:20251335-20252000	K562	blood:	n/a	n/a
23	RELA	chr2:20251191-20252101	GM19099	blood:	n/a	n/a
24	REST	chr2:20251595-20252077	PFSK-1	brain:	n/a	chr2:20251846-20251859 chr2:20251871-20251880
25	MYC	chr2:20251153-20252081	K562	blood:	n/a	n/a
26	TAF1	chr2:20251148-20252037	MCF-7	breast:	n/a	n/a
27	PML	chr2:20250934-20252246	GM12878	blood:	n/a	n/a
28	TAF1	chr2:20251618-20251975	GM12878	blood:	n/a	n/a
29	JUND	chr2:20251198-20252059	A549	lung:	n/a	chr2:20251519-20251528
30	CEBPB	chr2:20251632-20252083	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr2:20251740-20251890	HepG2	liver:	n/a	chr2:20251843-20251856
32	POLR2A	chr2:20251118-20252137	GM15510	blood:	n/a	n/a
33	NFIC	chr2:20251405-20252074	GM12878	blood:	n/a	n/a
34	POLR2A	chr2:20251102-20252058	HepG2	liver:	n/a	n/a
35	SP2	chr2:20251229-20251969	H1-hESC	embryonic stem cell:	n/a	chr2:20251483-20251493
36	CEBPD	chr2:20251212-20252051	K562	blood:	n/a	n/a
37	MXI1	chr2:20249818-20253177	Hela-S3	cervix:	n/a	n/a
38	ARID3A	chr2:20251447-20251959	K562	blood:	n/a	n/a
39	IRF1	chr2:20251222-20252033	K562	blood:	n/a	chr2:20251848-20251862
40	MAX	chr2:20251064-20252042	K562	blood:	n/a	n/a
41	TBL1XR1	chr2:20251207-20252069	K562	blood:	n/a	n/a
42	POLR2A	chr2:20251471-20252037	H1-hESC	embryonic stem cell:	n/a	n/a
43	REST	chr2:20249044-20253112	H1-neurons	neurons:	n/a	chr2:20250974-20250987 chr2:20251116-20251129 chr2:20251113-20251126 chr2:20252708-20252728 chr2:20251846-20251859 chr2:20251871-20251880
44	HNF4G	chr2:20251116-20252059	HepG2	liver:	n/a	chr2:20251814-20251826 chr2:20251809-20251831 chr2:20251813-20251826
45	EP300	chr2:20251344-20252171	A549	lung:	n/a	chr2:20251394-20251410
46	EGR1	chr2:20251047-20253113	HCT-116	colon:	n/a	chr2:20252760-20252771 chr2:20252758-20252773 chr2:20252760-20252770 chr2:20251427-20251436 chr2:20252760-20252769 chr2:20252758-20252772 chr2:20252759-20252772 chr2:20251844-20251857 chr2:20251393-20251406 chr2:20251849-20251859 chr2:20252760-20252770 chr2:20252759-20252772 chr2:20252759-20252772 chr2:20252756-20252770 chr2:20252759-20252772 chr2:20252760-20252771 chr2:20251390-20251404
47	YY1	chr2:20251586-20252060	GM12892	blood:	n/a	chr2:20251849-20251858 chr2:20251846-20251860
48	POLR2A	chr2:20250996-20252117	A549	lung:	n/a	n/a
49	POLR2A	chr2:20251056-20252058	GM12878	blood:	n/a	n/a
50	CEBPB	chr2:20251503-20252417	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20249888..20254017-chr2:20419396..20423263,3	MCF-7	breast:
2	chr2:20208645..20229804-chr2:20247969..20254330,37	MCF-7	breast:
3	chr2:20100261..20103746-chr2:20249026..20255152,7	K562	blood:
4	chr2:20233333..20235780-chr2:20251551..20254111,2	K562	blood:
5	chr2:20209928..20212604-chr2:20250418..20252144,2	MCF-7	breast:
6	chr1:28974783..28975713-chr2:20251159..20252070,2	Hela-S3	cervix:
7	chr19:13260810..13261697-chr2:20251318..20251943,2	Hela-S3	cervix:
8	chr2:20251385..20252181-chr6:74230268..74230794,2	Hela-S3	cervix:
9	chr16:27279568..27280111-chr2:20251412..20252038,2	Hela-S3	cervix:
10	chr14:24701099..24702081-chr2:20251545..20252199,2	Hela-S3	cervix:
11	chr2:20249637..20253449-chr2:20421472..20424385,3	MCF-7	breast:
12	chr14:81685801..81687372-chr2:20250284..20251948,2	MCF-7	breast:
13	chr2:20249233..20252415-chr2:20424056..20425890,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223734	TF binding region
ENSG00000271991	Chromatin interaction
ENSG00000160888	Chromatin interaction
ENSG00000104915	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000169189	Chromatin interaction
ENSG00000129559	Chromatin interaction
ENSG00000165417	Chromatin interaction
ENSG00000115884	Chromatin interaction
ENSG00000255526	Chromatin interaction
ENSG00000132031	Chromatin interaction
ENSG00000100938	Chromatin interaction
ENSG00000068697	Chromatin interaction
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1016317	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1016318	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs10175486	0.82[CEU][hapmap]
rs10203067	0.82[CEU][hapmap]
rs1028051	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12052278	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12233028	0.86[CEU][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12328613	0.87[CEU][hapmap]
rs12478941	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16987297	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2010930	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278528	0.87[CEU][hapmap]
rs2304589	0.87[CEU][hapmap]
rs3754908	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3769763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4666354	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55920955	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57887920	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57965673	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60557282	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62109428	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6717139	0.82[CEU][hapmap]
rs768377	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3754907	TTC32	cis	lymphoblastoid	seeQTL
rs3754907	HS1BP3	cis	parietal	SCAN
rs3754907	LOC130502	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20247400-20252600	Active TSS	Ovary	ovary
2	chr2:20248400-20252800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:20248400-20252800	Active TSS	Aorta	Aorta
4	chr2:20248600-20252800	Active TSS	Fetal Muscle Leg	muscle
5	chr2:20248600-20252800	Active TSS	Psoas Muscle	Psoas
6	chr2:20248600-20252800	Active TSS	Right Ventricle	heart
7	chr2:20248800-20252400	Active TSS	Fetal Intestine Large	intestine
8	chr2:20248800-20252400	Active TSS	Stomach Smooth Muscle	stomach
9	chr2:20248800-20252800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:20248800-20252800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:20248800-20252800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:20248800-20253000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:20249000-20252200	Active TSS	Fetal Thymus	thymus
14	chr2:20249000-20252200	Active TSS	GM12878-XiMat	blood
15	chr2:20249000-20252400	Active TSS	Colon Smooth Muscle	Colon
16	chr2:20249000-20252400	Active TSS	Fetal Lung	lung
17	chr2:20249000-20252400	Active TSS	HSMM	muscle
18	chr2:20249000-20252600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr2:20249000-20252600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:20249000-20252800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr2:20249000-20252800	Active TSS	H1 Cell Line	embryonic stem cell
22	chr2:20249000-20252800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:20249000-20252800	Active TSS	Fetal Kidney	kidney
24	chr2:20249000-20252800	Active TSS	NHDF-Ad	bronchial
25	chr2:20249000-20252800	Active TSS	NHLF	lung
26	chr2:20249000-20253200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:20249200-20252200	Active TSS	Fetal Stomach	stomach
28	chr2:20249200-20252600	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr2:20249200-20252600	Active TSS	Colonic Mucosa	Colon
30	chr2:20249200-20252800	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr2:20249200-20252800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:20249200-20252800	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr2:20249200-20252800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:20249200-20252800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:20249200-20252800	Active TSS	Fetal Muscle Trunk	muscle
36	chr2:20249200-20253000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:20249200-20253000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:20249200-20253000	Active TSS	HSMMtube	muscle
39	chr2:20249200-20253200	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr2:20249400-20251800	Active TSS	Placenta	Placenta
41	chr2:20249400-20252000	Active TSS	Lung	lung
42	chr2:20249400-20252000	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr2:20249400-20252200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:20249400-20252200	Active TSS	Muscle Satellite Cultured Cells	--
45	chr2:20249400-20252200	Active TSS	Left Ventricle	heart
46	chr2:20249400-20252200	Active TSS	HMEC	breast
47	chr2:20249400-20252400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:20249400-20252400	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr2:20249400-20252400	Active TSS	Esophagus	oesophagus
50	chr2:20249400-20252400	Active TSS	Pancreas	Pancrea

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