Variant report

Variant	rs2279761
Chromosome Location	chr3:98620372-98620373
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	RELA	chr3:98620286-98621055	GM15510	blood:	n/a	n/a
2	POLR2A	chr3:98618321-98620638	SK-N-SH	brain:	n/a	n/a
3	E2F4	chr3:98620041-98621122	MCF10A-Er-Src	breast:	n/a	n/a
4	E2F6	chr3:98620329-98620618	K562	blood:	n/a	n/a
5	ZBTB7A	chr3:98619769-98620573	K562	blood:	n/a	n/a
6	TAF1	chr3:98620116-98621139	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr3:98620089-98621148	HUVEC	blood vessel:	n/a	n/a
8	TAF1	chr3:98619761-98621074	SK-N-SH	brain:	n/a	n/a
9	MAZ	chr3:98619241-98621681	IMR90	lung:	n/a	n/a
10	HA-E2F1	chr3:98619996-98621050	Hela-S3	cervix:	n/a	n/a
11	IRF1	chr3:98620319-98621133	K562	blood:	n/a	chr3:98620770-98620784 chr3:98620574-98620588
12	CHD2	chr3:98620168-98621338	HepG2	liver:	n/a	chr3:98620361-98620371
13	POLR2A	chr3:98620315-98620669	K562	blood:	n/a	n/a
14	REST	chr3:98620325-98620597	SK-N-SH	brain:	n/a	chr3:98620358-98620368
15	CHD1	chr3:98619863-98620496	H1-hESC	embryonic stem cell:	n/a	chr3:98620361-98620371
16	ZBTB7A	chr3:98619646-98621127	ECC-1	luminal epithelium:	n/a	chr3:98620704-98620711
17	REST	chr3:98620339-98620711	PANC-1	pancreas:	n/a	chr3:98620358-98620368
18	EP300	chr3:98619783-98621301	SK-N-SH	brain:	n/a	chr3:98620499-98620515 chr3:98620885-98620892 chr3:98621042-98621056
19	POLR2A	chr3:98620219-98620677	HepG2	liver:	n/a	n/a
20	MAX	chr3:98619724-98621179	HepG2	liver:	n/a	n/a
21	POLR2A	chr3:98620258-98621168	PANC-1	pancreas:	n/a	n/a
22	REST	chr3:98619564-98621432	H1-neurons	neurons:	n/a	chr3:98620358-98620368
23	TAF1	chr3:98619078-98621229	A549	lung:	n/a	n/a
24	SP4	chr3:98620276-98621002	H1-hESC	embryonic stem cell:	n/a	chr3:98620574-98620590 chr3:98620772-98620783 chr3:98620576-98620592
25	JUND	chr3:98620031-98621069	K562	blood:	n/a	n/a
26	MAX	chr3:98619785-98621388	MCF-7	breast:	n/a	n/a
27	MXI1	chr3:98619865-98620887	H1-hESC	embryonic stem cell:	n/a	n/a
28	E2F6	chr3:98620149-98621214	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr3:98620235-98620616	GM12892	blood:	n/a	n/a
30	SIN3AK20	chr3:98620365-98620606	HepG2	liver:	n/a	n/a
31	ZBTB7A	chr3:98620219-98620612	HepG2	liver:	n/a	n/a
32	POLR2A	chr3:98619780-98621155	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr3:98620313-98620658	HepG2	liver:	n/a	n/a
34	UBTF	chr3:98619691-98621034	K562	blood:	n/a	n/a
35	UBTF	chr3:98619758-98621017	K562	blood:	n/a	n/a
36	USF2	chr3:98620282-98620462	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr3:98620223-98621195	SK-N-MC	brain:	n/a	n/a
38	GATA2	chr3:98619874-98621719	SH-SY5Y	brain:	n/a	chr3:98621157-98621168
39	BHLHE40	chr3:98620008-98621079	K562	blood:	n/a	chr3:98620210-98620226 chr3:98620251-98620267
40	POLR2A	chr3:98619866-98621061	HUVEC	blood vessel:	n/a	n/a
41	RCOR1	chr3:98619861-98621540	K562	blood:	n/a	n/a
42	TCF3	chr3:98620305-98620628	GM12878	blood:	n/a	n/a
43	REST	chr3:98619641-98621253	A549	lung:	n/a	chr3:98620358-98620368
44	YY1	chr3:98619985-98621054	GM12892	blood:	n/a	chr3:98620437-98620446 chr3:98620255-98620266 chr3:98620858-98620872 chr3:98620208-98620219
45	YY1	chr3:98620320-98620630	HCT-116	colon:	n/a	chr3:98620437-98620446
46	HA-E2F1	chr3:98619690-98621251	MCF-7	breast:	n/a	chr3:98619867-98619876
47	POLR2A	chr3:98619772-98621198	GM12892	blood:	n/a	n/a
48	POLR2A	chr3:98620283-98621046	HepG2	liver:	n/a	n/a
49	TAF1	chr3:98619982-98621010	HepG2	liver:	n/a	n/a
50	RAD21	chr3:98619508-98620623	IMR90	lung:	n/a	chr3:98620243-98620262 chr3:98620218-98620232

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98620298..98622928-chr3:98626076..98627807,2	MCF-7	breast:
2	chr15:65596821..65597625-chr3:98620042..98620956,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000239462	TF binding region
DCBLD2	TF binding region
ENSG00000207331	Chromatin interaction
ENSG00000200156	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1062196	0.84[EUR][1000 genomes]
rs12107050	0.83[EUR][1000 genomes]
rs12330170	0.83[EUR][1000 genomes]
rs12490832	0.83[EUR][1000 genomes]
rs13060012	0.83[EUR][1000 genomes]
rs1440150	0.85[EUR][1000 genomes]
rs1440151	0.82[EUR][1000 genomes]
rs1440152	0.81[EUR][1000 genomes]
rs17270593	0.82[EUR][1000 genomes]
rs1837500	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2119187	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2334230	0.82[EUR][1000 genomes]
rs2439214	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2439217	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2439220	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2439226	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2439229	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2454673	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2454676	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2454677	0.87[EUR][1000 genomes]
rs2454678	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2454680	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2454684	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2454691	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2470857	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2470860	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2470861	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2470864	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2470865	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2470867	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2470885	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28802000	0.86[EUR][1000 genomes]
rs2919236	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34234373	0.86[EUR][1000 genomes]
rs34558202	0.88[EUR][1000 genomes]
rs3755576	0.82[EUR][1000 genomes]
rs3772098	0.81[EUR][1000 genomes]
rs3772099	0.82[EUR][1000 genomes]
rs3772101	0.83[EUR][1000 genomes]
rs3772102	0.82[EUR][1000 genomes]
rs3821359	0.81[EUR][1000 genomes]
rs4269027	0.82[EUR][1000 genomes]
rs4425201	0.83[EUR][1000 genomes]
rs4426626	0.83[EUR][1000 genomes]
rs4494869	0.83[EUR][1000 genomes]
rs62278486	0.83[EUR][1000 genomes]
rs6785935	0.84[EUR][1000 genomes]
rs6788418	0.87[EUR][1000 genomes]
rs6790650	0.82[EUR][1000 genomes]
rs6793760	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6808116	0.82[EUR][1000 genomes]
rs704585	0.85[EUR][1000 genomes]
rs7431448	0.82[EUR][1000 genomes]
rs7611929	0.83[EUR][1000 genomes]
rs7612036	0.83[EUR][1000 genomes]
rs7612605	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7616275	0.86[EUR][1000 genomes]
rs7630800	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs828609	0.85[EUR][1000 genomes]
rs844160	0.82[EUR][1000 genomes]
rs9289683	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9289685	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9811305	0.82[EUR][1000 genomes]
rs9820384	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9845558	0.87[EUR][1000 genomes]
rs9860216	0.84[EUR][1000 genomes]
rs9866570	0.82[EUR][1000 genomes]
rs9872152	0.82[EUR][1000 genomes]
rs9873932	0.85[EUR][1000 genomes]
rs9878392	0.82[EUR][1000 genomes]
rs9881519	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2279761	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL
rs2279761	DCBLD2	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98615000-98620400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:98615600-98621200	Active TSS	NHLF	lung
3	chr3:98616600-98621400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:98616800-98621200	Active TSS	NHDF-Ad	bronchial
5	chr3:98617400-98621200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:98617400-98622000	Active TSS	Right Ventricle	heart
7	chr3:98617600-98621200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr3:98618200-98621800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:98618400-98621200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr3:98618400-98621200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr3:98618400-98621200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:98618400-98621200	Active TSS	Fetal Kidney	kidney
13	chr3:98618400-98621200	Active TSS	GM12878-XiMat	blood
14	chr3:98618400-98621400	Active TSS	Left Ventricle	heart
15	chr3:98618400-98621600	Active TSS	Right Atrium	heart
16	chr3:98618400-98621800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:98618600-98621200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:98618600-98621400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:98618600-98621600	Active TSS	Ovary	ovary
20	chr3:98618600-98621800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr3:98618600-98621800	Active TSS	HSMMtube	muscle
22	chr3:98618800-98621200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:98618800-98621200	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr3:98618800-98621200	Active TSS	Stomach Smooth Muscle	stomach
25	chr3:98618800-98621400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:98618800-98621600	Active TSS	Psoas Muscle	Psoas
27	chr3:98618800-98621800	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr3:98618800-98622200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:98619000-98621200	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr3:98619000-98621200	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr3:98619000-98621200	Active TSS	HSMM	muscle
32	chr3:98619000-98621600	Active TSS	Fetal Muscle Trunk	muscle
33	chr3:98619200-98620400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:98619200-98620800	Active TSS	HepG2	liver
35	chr3:98619200-98621200	Active TSS	Brain Substantia Nigra	brain
36	chr3:98619200-98621200	Active TSS	HMEC	breast
37	chr3:98619200-98621200	Active TSS	K562	blood
38	chr3:98619200-98621400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr3:98619200-98621600	Active TSS	H9 Cell Line	embryonic stem cell
40	chr3:98619200-98621600	Active TSS	Aorta	Aorta
41	chr3:98619400-98620400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:98619400-98621000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:98619400-98621200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:98619400-98621200	Active TSS	Fetal Lung	lung
45	chr3:98619400-98621200	Active TSS	Lung	lung
46	chr3:98619400-98621200	Active TSS	A549	lung
47	chr3:98619400-98621400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:98619400-98621400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:98619400-98621400	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr3:98619400-98621600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links