Variant report

Variant	rs11949545
Chromosome Location	chr5:118788606-118788607
allele	C/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	GATA3	chr5:118788514-118788822	SH-SY5Y	brain:	n/a	chr5:118788628-118788637 chr5:118788628-118788635 chr5:118788627-118788637 chr5:118788627-118788635
2	ZKSCAN1	chr5:118788221-118788692	Hela-S3	cervix:	n/a	n/a
3	BHLHE40	chr5:118787790-118788659	K562	blood:	n/a	n/a
4	HDAC2	chr5:118788410-118788985	HepG2	liver:	n/a	chr5:118788627-118788636
5	GATA3	chr5:118788462-118789113	MCF-7	breast:	n/a	chr5:118788628-118788637 chr5:118788628-118788635 chr5:118788847-118788859 chr5:118788627-118788637 chr5:118788627-118788635
6	ZMIZ1	chr5:118787887-118789066	K562	blood:	n/a	n/a
7	TAF7	chr5:118788051-118788693	H1-hESC	embryonic stem cell:	n/a	n/a
8	NRF1	chr5:118788075-118788607	GM12878	blood:	n/a	chr5:118788401-118788412
9	POLR2A	chr5:118787975-118788675	MCF-7	breast:	n/a	n/a
10	JUND	chr5:118787927-118788809	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr5:118787994-118788661	A549	lung:	n/a	n/a
12	POLR2A	chr5:118788052-118788666	GM12891	blood:	n/a	n/a
13	TBP	chr5:118787892-118788645	Hela-S3	cervix:	n/a	n/a
14	POU2F2	chr5:118788091-118788633	GM12891	blood:	n/a	n/a
15	HEY1	chr5:118787982-118788617	K562	blood:	n/a	n/a
16	SMC3	chr5:118787920-118788870	Hela-S3	cervix:	n/a	n/a
17	MAX	chr5:118788066-118788649	GM12878	blood:	n/a	n/a
18	POLR2A	chr5:118787917-118788684	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:118788015-118789066	K562	blood:	n/a	n/a
20	POLR2A	chr5:118787894-118788776	Hela-S3	cervix:	n/a	n/a
21	TCF7L2	chr5:118788043-118789030	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr5:118788441-118788848	HepG2	liver:	n/a	chr5:118788595-118788608 chr5:118788597-118788608 chr5:118788595-118788606
23	POLR2A	chr5:118788278-118788658	GM12892	blood:	n/a	n/a
24	MAX	chr5:118787855-118788619	A549	lung:	n/a	n/a
25	POLR2A	chr5:118787887-118788719	HCT-116	colon:	n/a	n/a
26	ZNF143	chr5:118787785-118788747	GM12878	blood:	n/a	chr5:118788098-118788116 chr5:118788102-118788121 chr5:118788100-118788109 chr5:118788098-118788107 chr5:118788719-118788729
27	ZNF263	chr5:118787940-118788639	HEK293-T-REx	kidney:	n/a	n/a
28	CREB1	chr5:118787864-118789123	HepG2	liver:	n/a	n/a
29	NFIC	chr5:118787982-118788695	ECC-1	luminal epithelium:	n/a	n/a
30	TCF7L2	chr5:118787998-118788697	HCT-116	colon:	n/a	n/a
31	POLR2A	chr5:118787809-118789070	HepG2	liver:	n/a	n/a
32	MYC	chr5:118788556-118788614	HepG2	liver:	n/a	n/a
33	TCF12	chr5:118788206-118788700	H1-hESC	embryonic stem cell:	n/a	chr5:118788367-118788377 chr5:118788371-118788378
34	PML	chr5:118787867-118788807	GM12878	blood:	n/a	n/a
35	CEBPB	chr5:118788367-118788787	MCF-7	breast:	n/a	chr5:118788595-118788608 chr5:118788597-118788608 chr5:118788595-118788606
36	GATA3	chr5:118788116-118788961	MCF-7	breast:	n/a	chr5:118788628-118788637 chr5:118788628-118788635 chr5:118788847-118788859 chr5:118788627-118788637 chr5:118788627-118788635
37	CHD2	chr5:118787988-118788703	H1-hESC	embryonic stem cell:	n/a	n/a
38	SIN3A	chr5:118788189-118788781	GM12878	blood:	n/a	n/a
39	GATA1	chr5:118788092-118789851	PBDE	blood:	n/a	chr5:118788628-118788637 chr5:118788628-118788635 chr5:118788847-118788859 chr5:118788627-118788637
40	CEBPB	chr5:118788415-118788783	A549	lung:	n/a	chr5:118788595-118788608 chr5:118788597-118788608 chr5:118788595-118788606
41	POLR2A	chr5:118787921-118788612	H1-hESC	embryonic stem cell:	n/a	n/a
42	RUNX3	chr5:118787929-118788737	GM12878	blood:	n/a	n/a
43	EP300	chr5:118788170-118788806	HepG2	liver:	n/a	n/a
44	MAZ	chr5:118787964-118788928	K562	blood:	n/a	n/a
45	CEBPB	chr5:118788469-118788736	HepG2	liver:	n/a	chr5:118788595-118788608 chr5:118788597-118788608 chr5:118788595-118788606
46	HA-E2F1	chr5:118787771-118789082	MCF-7	breast:	n/a	chr5:118788719-118788729
47	CCNT2	chr5:118788090-118788668	K562	blood:	n/a	n/a
48	YY1	chr5:118787855-118788609	ECC-1	luminal epithelium:	n/a	chr5:118788038-118788060
49	MAX	chr5:118788187-118788768	HepG2	liver:	n/a	n/a
50	TBP	chr5:118787859-118788760	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:118323861..118326778-chr5:118787539..118789741,2	MCF-7	breast:
2	chr5:118788483..118791355-chr5:118802793..118805177,3	K562	blood:
3	chr5:118787302..118789344-chr5:118814419..118817189,2	K562	blood:
4	chr22:50354001..50354626-chr5:118788080..118788710,2	HCT-116	colon:

Variant related genes	Relation type
HSD17B4	TF binding region
ENSG00000198355	Chromatin interaction
ENSG00000133835	Chromatin interaction
ENSG00000169570	Chromatin interaction
ENSG00000239084	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10067861	1.00[EUR][1000 genomes]
rs10073635	1.00[EUR][1000 genomes]
rs10478420	1.00[EUR][1000 genomes]
rs11948865	1.00[EUR][1000 genomes]
rs11951660	1.00[EUR][1000 genomes]
rs11952687	1.00[EUR][1000 genomes]
rs11955089	1.00[EUR][1000 genomes]
rs11956487	1.00[EUR][1000 genomes]
rs11959643	1.00[EUR][1000 genomes]
rs11959779	1.00[EUR][1000 genomes]
rs12714	1.00[EUR][1000 genomes]
rs1428437	1.00[EUR][1000 genomes]
rs2560723	1.00[EUR][1000 genomes]
rs28943594	1.00[EUR][1000 genomes]
rs35182344	1.00[EUR][1000 genomes]
rs35764784	1.00[EUR][1000 genomes]
rs3843986	1.00[EUR][1000 genomes]
rs3850203	1.00[EUR][1000 genomes]
rs3850204	1.00[EUR][1000 genomes]
rs4099736	1.00[EUR][1000 genomes]
rs57270573	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57592998	1.00[EUR][1000 genomes]
rs57990091	1.00[EUR][1000 genomes]
rs58527989	1.00[EUR][1000 genomes]
rs59177585	1.00[EUR][1000 genomes]
rs59940947	1.00[EUR][1000 genomes]
rs60069733	1.00[EUR][1000 genomes]
rs60684792	1.00[EUR][1000 genomes]
rs60871537	1.00[EUR][1000 genomes]
rs61460721	1.00[EUR][1000 genomes]
rs61645108	1.00[EUR][1000 genomes]
rs6868057	1.00[EUR][1000 genomes]
rs73235250	1.00[EUR][1000 genomes]
rs73235258	1.00[EUR][1000 genomes]
rs73236713	1.00[EUR][1000 genomes]
rs73236767	1.00[EUR][1000 genomes]
rs73236771	1.00[EUR][1000 genomes]
rs73237264	1.00[EUR][1000 genomes]
rs73238798	1.00[EUR][1000 genomes]
rs73240903	1.00[EUR][1000 genomes]
rs73241213	1.00[EUR][1000 genomes]
rs73241292	1.00[EUR][1000 genomes]
rs73243205	1.00[EUR][1000 genomes]
rs73246514	1.00[EUR][1000 genomes]
rs73246536	1.00[EUR][1000 genomes]
rs73249960	1.00[EUR][1000 genomes]
rs73249990	1.00[EUR][1000 genomes]
rs73250002	1.00[EUR][1000 genomes]
rs73251677	1.00[EUR][1000 genomes]
rs73256182	1.00[EUR][1000 genomes]
rs7708761	1.00[EUR][1000 genomes]
rs7711431	1.00[EUR][1000 genomes]
rs7711926	1.00[EUR][1000 genomes]
rs7723718	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv4974	chr5:118750259-118795376	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Flanking 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	12 gene(s)	inside rSNPs	diseases
4	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118787200-118789000	Active TSS	Brain Anterior Caudate	brain
2	chr5:118787400-118789200	Active TSS	Brain Hippocampus Middle	brain
3	chr5:118787400-118789400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr5:118787600-118788800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:118787600-118788800	Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr5:118787600-118788800	Active TSS	Brain Cingulate Gyrus	brain
7	chr5:118787600-118789000	Active TSS	Brain Angular Gyrus	brain
8	chr5:118787600-118789000	Active TSS	Fetal Heart	heart
9	chr5:118787600-118789200	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr5:118787600-118789200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:118787600-118789200	Active TSS	Brain Substantia Nigra	brain
12	chr5:118787600-118789200	Active TSS	NHEK	skin
13	chr5:118787800-118788800	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr5:118787800-118788800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr5:118787800-118788800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr5:118787800-118788800	Active TSS	Fetal Intestine Large	intestine
17	chr5:118787800-118788800	Active TSS	Rectal Mucosa Donor 31	rectum
18	chr5:118787800-118789000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:118787800-118789000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:118787800-118789000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:118787800-118789000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:118787800-118789000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr5:118787800-118789000	Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr5:118787800-118789000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:118787800-118789000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:118787800-118789000	Active TSS	Duodenum Mucosa	Duodenum
27	chr5:118787800-118789000	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr5:118787800-118789000	Active TSS	Fetal Kidney	kidney
29	chr5:118787800-118789000	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr5:118787800-118789000	Active TSS	Fetal Lung	lung
31	chr5:118787800-118789000	Active TSS	Fetal Muscle Trunk	muscle
32	chr5:118787800-118789000	Active TSS	Ovary	ovary
33	chr5:118787800-118789000	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr5:118787800-118789000	Active TSS	Rectal Smooth Muscle	rectum
35	chr5:118787800-118789000	Active TSS	A549	lung
36	chr5:118787800-118789000	Active TSS	HMEC	breast
37	chr5:118787800-118789200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:118787800-118789200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:118787800-118789200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:118787800-118789200	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr5:118787800-118789200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:118787800-118789200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:118787800-118789200	Active TSS	Colonic Mucosa	Colon
44	chr5:118787800-118789200	Active TSS	Fetal Stomach	stomach
45	chr5:118787800-118789200	Active TSS	Left Ventricle	heart
46	chr5:118787800-118789200	Active TSS	Pancreas	Pancrea
47	chr5:118787800-118789200	Active TSS	Thymus	Thymus
48	chr5:118787800-118789200	Active TSS	HSMM	muscle
49	chr5:118787800-118789200	Active TSS	NHDF-Ad	bronchial
50	chr5:118787800-118789200	Active TSS	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links