Variant report

Variant	rs3754908
Chromosome Location	chr2:20252270-20252271
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	CUX1	chr2:20252237-20253184	K562	blood:	n/a	n/a
2	YY1	chr2:20251126-20252395	SK-N-SH	brain:	n/a	chr2:20251849-20251858 chr2:20251846-20251860
3	TAF1	chr2:20250346-20252400	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr2:20251080-20252413	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr2:20251120-20252378	HepG2	liver:	n/a	n/a
6	MXI1	chr2:20249818-20253177	Hela-S3	cervix:	n/a	n/a
7	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
8	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
9	CEBPB	chr2:20251503-20252417	A549	lung:	n/a	n/a
10	STAT3	chr2:20251358-20253018	MCF10A-Er-Src	breast:	n/a	chr2:20252736-20252747
11	POLR2A	chr2:20251173-20252270	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr2:20251019-20252669	A549	lung:	n/a	n/a
13	POLR2A	chr2:20251011-20252554	H1-neurons	neurons:	n/a	n/a
14	FOS	chr2:20252219-20252896	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr2:20251133-20252295	Hela-S3	cervix:	n/a	n/a
16	E2F4	chr2:20251297-20252955	MCF10A-Er-Src	breast:	n/a	chr2:20251849-20251858 chr2:20251853-20251863 chr2:20251427-20251436
17	JUND	chr2:20251440-20252467	H1-hESC	embryonic stem cell:	n/a	chr2:20251519-20251528
18	GTF2F1	chr2:20251187-20252870	Hela-S3	cervix:	n/a	n/a
19	SIN3AK20	chr2:20251060-20252473	A549	lung:	n/a	n/a
20	MBD4	chr2:20251035-20252739	HepG2	liver:	n/a	n/a
21	CTCF	chr2:20252200-20252350	GM12873	blood:	n/a	n/a
22	MAX	chr2:20250917-20252620	HepG2	liver:	n/a	n/a
23	POLR2A	chr2:20250165-20252913	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr2:20250958-20252994	U87	brain:	n/a	n/a
25	SMARCB1	chr2:20250382-20252307	Hela-S3	cervix:	n/a	n/a
26	MAX	chr2:20251047-20252371	HepG2	liver:	n/a	n/a
27	CHD1	chr2:20247605-20252898	IMR90	lung:	n/a	n/a
28	TBP	chr2:20251210-20252984	Hela-S3	cervix:	n/a	n/a
29	ZKSCAN1	chr2:20251205-20252328	Hela-S3	cervix:	n/a	n/a
30	MYC	chr2:20252263-20252935	MCF10A-Er-Src	breast:	n/a	n/a
31	TAF1	chr2:20250958-20252448	A549	lung:	n/a	n/a
32	YY1	chr2:20251552-20252386	H1-hESC	embryonic stem cell:	n/a	chr2:20251849-20251858 chr2:20251846-20251860
33	SIN3AK20	chr2:20251058-20252459	A549	lung:	n/a	n/a
34	JUND	chr2:20251188-20252951	K562	blood:	n/a	chr2:20251519-20251528
35	POLR2A	chr2:20249848-20252962	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr2:20251056-20252335	PFSK-1	brain:	n/a	n/a
37	EP300	chr2:20251589-20252390	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr2:20251061-20252507	Hela-S3	cervix:	n/a	n/a
39	ETS1	chr2:20251529-20252288	A549	lung:	n/a	chr2:20251847-20251858
40	POLR2A	chr2:20251065-20252287	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr2:20249628-20252299	K562	blood:	n/a	n/a
42	TAF1	chr2:20251080-20252458	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr2:20250931-20252279	HUVEC	blood vessel:	n/a	n/a
44	MYBL2	chr2:20250992-20252682	HepG2	liver:	n/a	n/a
45	TAF1	chr2:20251141-20252349	H1-neurons	neurons:	n/a	n/a
46	YY1	chr2:20251058-20252322	A549	lung:	n/a	chr2:20251849-20251858 chr2:20251846-20251860
47	FOSL2	chr2:20251211-20252804	A549	lung:	n/a	chr2:20251519-20251528
48	YY1	chr2:20251546-20252481	SK-N-SH_RA	brain:	n/a	chr2:20251849-20251858 chr2:20251846-20251860
49	MAX	chr2:20251118-20252325	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr2:20251085-20252421	H1-neurons	neurons:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:20252225-20252275	GM19239	blood:	n/a
2	chr2:20252225-20252275	CMK	blood:	n/a
3	chr2:20252225-20252275	PFSK-1	brain:	n/a
4	chr2:20252254-20252304	HepG2	liver:	n/a
5	chr2:20252254-20252304	HEK293	kidney:	embryo
6	chr2:20252254-20252304	SAEC	small airway:	n/a
7	chr2:20252254-20252304	ECC-1	luminal epithelium:	n/a
8	chr2:20252254-20252304	Jurkat	blood:	n/a
9	chr2:20252225-20252275	MCF10A-Er-Src	breast:	n/a
10	chr2:20252225-20252275	HUVEC	blood vessel:	n/a
11	chr2:20252225-20252275	BE2_C	brain:	n/a
12	chr2:20252225-20252275	SK-N-SH	brain:	n/a
13	chr2:20252254-20252304	HUVEC	blood vessel:	n/a
14	chr2:20252225-20252275	K562	blood:	n/a
15	chr2:20252254-20252304	AG04449	skin:	fetal
16	chr2:20252225-20252275	HRE	kidney:	n/a
17	chr2:20252225-20252275	AG04450	lung:	fetal
18	chr2:20252254-20252304	NH-A	brain:	n/a
19	chr2:20252225-20252275	A549	lung:	n/a
20	chr2:20252225-20252275	HMEC	breast:	n/a
21	chr2:20252225-20252275	NH-A	brain:	n/a
22	chr2:20252254-20252304	MCF10A-Er-Src	breast:	n/a
23	chr2:20252254-20252304	NHBE	bronchial:	n/a
24	chr2:20252225-20252275	NHBE	bronchial:	n/a
25	chr2:20252254-20252304	NHDF-neo	bronchial:	n/a
26	chr2:20252225-20252275	HRPEpiC	eye:	n/a
27	chr2:20252225-20252275	PrEC	prostate:	n/a
28	chr2:20252254-20252304	GM06990	blood:	n/a
29	chr2:20252225-20252275	HEEpiC	esophagus:	n/a
30	chr2:20252225-20252275	H1-hESC	embryonic stem cell:	embryo
31	chr2:20252254-20252304	ovcar-3	ovarian:	n/a
32	chr2:20252225-20252275	MCF-7	breast:	n/a
33	chr2:20252254-20252304	SK-N-MC	brain:	n/a
34	chr2:20252254-20252304	NB4	blood:	n/a
35	chr2:20252254-20252304	HCT-116	colon:	n/a
36	chr2:20252225-20252275	GM12878	blood:	n/a
37	chr2:20252225-20252275	SKMC	muscle:	n/a
38	chr2:20252225-20252275	HNPCEpiC	eye:	n/a
39	chr2:20252225-20252275	PANC-1	pancreas:	n/a
40	chr2:20252254-20252304	HL-60	blood:	n/a
41	chr2:20252254-20252304	Hela-S3	cervix:	n/a
42	chr2:20252225-20252275	ovcar-3	ovarian:	n/a
43	chr2:20252254-20252304	HAEpiC	amniotic membrane:	n/a
44	chr2:20252225-20252275	BJ	skin:	n/a
45	chr2:20252254-20252304	HRCEpiC	kidney:	n/a
46	chr2:20252225-20252275	U87	brain:	n/a
47	chr2:20252254-20252304	HMEC	breast:	n/a
48	chr2:20252254-20252304	GM19239	blood:	n/a
49	chr2:20252225-20252275	AG04449	skin:	fetal
50	chr2:20252254-20252304	HCPEpiC	choroid plexus:	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	chr2:20251925..20253878-chr2:20548760..20551591,2	K562	blood:
6	chr2:20252121..20254542-chr2:20263523..20265245,3	K562	blood:
7	chr2:20249637..20253449-chr2:20421472..20424385,3	MCF-7	breast:
8	chr2:20154730..20157342-chr2:20251930..20254193,3	MCF-7	breast:
9	chr2:20249233..20252415-chr2:20424056..20425890,4	MCF-7	breast:

Variant related genes	Relation type
LAPTM4A	TF binding region
LAPTM4A	CpG island
ENSG00000055917	Chromatin interaction
ENSG00000115884	Chromatin interaction
ENSG00000271991	Chromatin interaction
ENSG00000068697	Chromatin interaction
ENSG00000132031	Chromatin interaction
ENSG00000183891	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1016317	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1016318	0.86[CHD][hapmap]
rs10175486	0.82[CEU][hapmap]
rs10203067	0.82[CEU][hapmap]
rs1028051	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12052278	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12233028	0.86[CEU][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12328613	0.87[CEU][hapmap]
rs12478941	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs16987297	0.82[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs2010930	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278528	0.87[CEU][hapmap]
rs2304589	0.87[CEU][hapmap]
rs3754907	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];0.91[CHB][hapmap];0.91[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4666354	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55920955	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57887920	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57965673	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60557282	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62109428	0.82[EUR][1000 genomes]
rs6717139	0.82[CEU][hapmap]
rs768377	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3754908	HS1BP3	cis	parietal	SCAN
rs3754908	LOC130502	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 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	chr2:20249000-20252400	Active TSS	Colon Smooth Muscle	Colon
14	chr2:20249000-20252400	Active TSS	Fetal Lung	lung
15	chr2:20249000-20252400	Active TSS	HSMM	muscle
16	chr2:20249000-20252600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr2:20249000-20252600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:20249000-20252800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr2:20249000-20252800	Active TSS	H1 Cell Line	embryonic stem cell
20	chr2:20249000-20252800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:20249000-20252800	Active TSS	Fetal Kidney	kidney
22	chr2:20249000-20252800	Active TSS	NHDF-Ad	bronchial
23	chr2:20249000-20252800	Active TSS	NHLF	lung
24	chr2:20249000-20253200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:20249200-20252600	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr2:20249200-20252600	Active TSS	Colonic Mucosa	Colon
27	chr2:20249200-20252800	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr2:20249200-20252800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:20249200-20252800	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr2:20249200-20252800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:20249200-20252800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:20249200-20252800	Active TSS	Fetal Muscle Trunk	muscle
33	chr2:20249200-20253000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:20249200-20253000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:20249200-20253000	Active TSS	HSMMtube	muscle
36	chr2:20249200-20253200	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr2:20249400-20252400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:20249400-20252400	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr2:20249400-20252400	Active TSS	Esophagus	oesophagus
40	chr2:20249400-20252400	Active TSS	Pancreas	Pancrea
41	chr2:20249400-20252600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:20249400-20252600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:20249400-20252600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:20249400-20252600	Active TSS	Fetal Brain Female	brain
45	chr2:20249400-20252600	Active TSS	Placenta Amnion	Placenta Amnion
46	chr2:20249400-20252800	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr2:20249400-20252800	Active TSS	Fetal Intestine Small	intestine
48	chr2:20249400-20253000	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr2:20249400-20253000	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr2:20249600-20252600	Active TSS	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links