Variant report

Variant	rs3755743
Chromosome Location	chr3:112709373-112709374
allele	A/C
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	MBD4	chr3:112709307-112710245	HepG2	liver:	n/a	n/a
2	KAP1	chr3:112709366-112710536	HEK293	kidney:	n/a	n/a
3	MXI1	chr3:112709359-112710470	GM12878	blood:	n/a	n/a
4	MAX	chr3:112709326-112710363	H1-hESC	embryonic stem cell:	n/a	n/a
5	GABPA	chr3:112709364-112710487	A549	lung:	n/a	chr3:112709785-112709796
6	PBX3	chr3:112709199-112710282	A549	lung:	n/a	n/a
7	MXI1	chr3:112709337-112710650	IMR90	lung:	n/a	n/a
8	NRF1	chr3:112709193-112710633	SK-N-SH	brain:	n/a	chr3:112709785-112709796 chr3:112709785-112709796
9	BCL3	chr3:112709303-112710379	A549	lung:	n/a	chr3:112709664-112709677
10	E2F6	chr3:112709272-112710407	H1-hESC	embryonic stem cell:	n/a	chr3:112709691-112709702
11	PML	chr3:112709267-112710614	GM12878	blood:	n/a	n/a
12	BRCA1	chr3:112709305-112710939	Hela-S3	cervix:	n/a	n/a
13	TEAD4	chr3:112709313-112709766	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr3:112709189-112710548	A549	lung:	n/a	n/a
15	MAX	chr3:112709342-112710356	SK-N-SH	brain:	n/a	n/a
16	ZEB1	chr3:112709355-112710586	HepG2	liver:	n/a	chr3:112710041-112710050
17	CEBPB	chr3:112709104-112709417	IMR90	lung:	n/a	n/a
18	GABPA	chr3:112709350-112710681	MCF-7	breast:	n/a	chr3:112709785-112709796
19	MAX	chr3:112709352-112710292	K562	blood:	n/a	n/a
20	MYBL2	chr3:112709316-112710393	HepG2	liver:	n/a	chr3:112709593-112709607 chr3:112709591-112709601
21	MAX	chr3:112709314-112710499	HCT-116	colon:	n/a	n/a
22	POLR2A	chr3:112709328-112710485	U87	brain:	n/a	n/a
23	POLR2A	chr3:112709199-112710339	HL-60	blood:	n/a	n/a
24	POLR2A	chr3:112708934-112710486	K562	blood:	n/a	n/a
25	POLR2A	chr3:112709328-112710427	H1-hESC	embryonic stem cell:	n/a	n/a
26	STAT3	chr3:112709212-112710279	MCF10A-Er-Src	breast:	n/a	chr3:112709506-112709515 chr3:112709830-112709841 chr3:112709832-112709840 chr3:112709507-112709516
27	POLR2A	chr3:112709317-112710447	K562	blood:	n/a	n/a
28	MAX	chr3:112709371-112710491	HepG2	liver:	n/a	n/a
29	E2F6	chr3:112709343-112710349	K562	blood:	n/a	chr3:112709691-112709702
30	MAX	chr3:112709244-112710423	HCT-116	colon:	n/a	n/a
31	POLR2A	chr3:112709312-112710470	SK-N-MC	brain:	n/a	n/a
32	CHD1	chr3:112709370-112710176	H1-hESC	embryonic stem cell:	n/a	chr3:112709691-112709701
33	POLR2A	chr3:112709314-112710514	HUVEC	blood vessel:	n/a	n/a
34	E2F6	chr3:112709364-112710305	H1-hESC	embryonic stem cell:	n/a	chr3:112709691-112709702
35	MAX	chr3:112709275-112710472	A549	lung:	n/a	n/a
36	POLR2A	chr3:112709328-112710491	U87	brain:	n/a	n/a
37	TEAD4	chr3:112709275-112710323	K562	blood:	n/a	n/a
38	HCFC1	chr3:112709171-112710945	Hela-S3	cervix:	n/a	n/a
39	E2F6	chr3:112709231-112710388	A549	lung:	n/a	chr3:112709691-112709702
40	POLR2A	chr3:112709274-112710434	GM19099	blood:	n/a	n/a
41	MAX	chr3:112709356-112710051	MCF-7	breast:	n/a	n/a
42	E2F4	chr3:112709165-112710750	MCF10A-Er-Src	breast:	n/a	chr3:112709773-112709784
43	MAX	chr3:112709315-112710559	Hela-S3	cervix:	n/a	n/a
44	MYC	chr3:112709361-112710301	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr3:112709283-112710507	GM12891	blood:	n/a	n/a
46	TBP	chr3:112709343-112710487	GM12878	blood:	n/a	n/a
47	MAX	chr3:112709294-112710416	SK-N-SH	brain:	n/a	n/a
48	MAX	chr3:112709335-112710442	ECC-1	luminal epithelium:	n/a	n/a
49	CBX3	chr3:112709332-112710321	K562	blood:	n/a	n/a
50	MYC	chr3:112709311-112710253	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:112358718..112361602-chr3:112709202..112711684,5	MCF-7	breast:
2	chr3:112709241..112710011-chr3:112737824..112738662,2	HCT-116	colon:
3	chr3:112708559..112710573-chr3:112736590..112739999,3	K562	blood:
4	chr3:112354988..112357166-chr3:112709171..112711334,2	MCF-7	breast:
5	chr3:112357488..112363507-chr3:112707947..112711649,7	K562	blood:
6	chr3:112358506..112363260-chr3:112706755..112711649,8	K562	blood:
7	chr3:112709111..112712767-chr3:112725826..112728376,3	K562	blood:
8	chr3:112358478..112360877-chr3:112708365..112711089,3	MCF-7	breast:
9	chr3:112708671..112711453-chr3:112735992..112738475,2	K562	blood:
10	chr3:112708547..112711309-chr3:112736671..112738787,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf17-2	chr3:112709294-112710000	ENSG00000272844.1

Variant related genes	Relation type
GTPBP8	TF binding region
ENSG00000091986	Chromatin interaction
ENSG00000163608	Chromatin interaction
ENSG00000240057	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11920110	1.00[AMR][1000 genomes]
rs16860242	0.82[CHB][hapmap]
rs2306858	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732813	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732814	0.87[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3736593	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816832	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57163779	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57916867	0.99[ASN][1000 genomes]
rs58720412	1.00[AMR][1000 genomes]
rs59998761	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60626674	0.97[ASN][1000 genomes]
rs6770507	0.82[CHB][hapmap]
rs72952155	0.81[ASN][1000 genomes]
rs72952157	0.81[ASN][1000 genomes]
rs72952158	0.97[ASN][1000 genomes]
rs72952159	1.00[AMR][1000 genomes]
rs72952160	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72952161	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72952168	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952169	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952171	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952172	1.00[ASN][1000 genomes]
rs72952182	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72952188	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72952190	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72952192	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7651481	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864286	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1843165	chr3:112628205-112740145	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3755743	GTPBP8	cis	multi-tissue	Pritchard

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112702200-112709400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:112703800-112709400	Weak transcription	Primary B cells from cord blood	blood
3	chr3:112703800-112709400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr3:112703800-112709400	Weak transcription	Gastric	stomach
5	chr3:112703800-112709400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:112704000-112709400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:112704000-112709400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:112704000-112709400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:112704000-112709400	Weak transcription	Placenta	Placenta
10	chr3:112704000-112709400	Weak transcription	Fetal Thymus	thymus
11	chr3:112704000-112709400	Weak transcription	Psoas Muscle	Psoas
12	chr3:112704000-112709400	Weak transcription	Thymus	Thymus
13	chr3:112706800-112709400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:112707000-112709400	Weak transcription	Pancreas	Pancrea
15	chr3:112707200-112709400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:112708800-112709400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:112708800-112709400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:112709000-112709400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr3:112709000-112709600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:112709000-112710000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:112709000-112710800	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr3:112709000-112711200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr3:112709000-112711600	Active TSS	K562	blood
24	chr3:112709200-112709400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:112709200-112709400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr3:112709200-112709400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:112709200-112709400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:112709200-112709400	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr3:112709200-112709400	Active TSS	Primary T cells fromperipheralblood	blood
30	chr3:112709200-112709400	Active TSS	Primary hematopoietic stem cells	blood
31	chr3:112709200-112709400	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr3:112709200-112709400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:112709200-112709400	Enhancers	Muscle Satellite Cultured Cells	--
34	chr3:112709200-112709400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr3:112709200-112709400	Enhancers	Fetal Intestine Large	intestine
36	chr3:112709200-112709400	Enhancers	Fetal Lung	lung
37	chr3:112709200-112709400	Enhancers	Stomach Mucosa	stomach
38	chr3:112709200-112709400	Enhancers	HSMM	muscle
39	chr3:112709200-112709400	Enhancers	HSMMtube	muscle
40	chr3:112709200-112709600	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr3:112709200-112709600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr3:112709200-112709600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr3:112709200-112709600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:112709200-112709600	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr3:112709200-112709600	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr3:112709200-112709600	Flanking Active TSS	Hela-S3	cervix
47	chr3:112709200-112709600	Flanking Active TSS	HMEC	breast
48	chr3:112709200-112709600	Flanking Active TSS	NHEK	skin
49	chr3:112709200-112709600	Flanking Active TSS	Osteobl	bone
50	chr3:112709200-112709800	Flanking 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