Variant report

Variant	rs73346092
Chromosome Location	chr12:58003775-58003776
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr12:58003531-58004020	H1-hESC	embryonic stem cell:	n/a	chr12:58003614-58003627 chr12:58003874-58003884 chr12:58003888-58003901 chr12:58003871-58003884
2	CTBP2	chr12:58002815-58004441	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZMIZ1	chr12:58003662-58003816	K562	blood:	n/a	n/a
4	POLR2A	chr12:58003592-58003843	ECC-1	luminal epithelium:	n/a	n/a
5	SIN3A	chr12:58002857-58005570	H1-hESC	embryonic stem cell:	n/a	chr12:58004864-58004877
6	SIN3AK20	chr12:58003550-58004384	H1-hESC	embryonic stem cell:	n/a	n/a
7	TEAD4	chr12:58003706-58004108	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZBTB7A	chr12:58003767-58004183	K562	blood:	n/a	chr12:58003955-58003964
9	ZNF143	chr12:58002810-58004254	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr12:58003701-58003813	ProgFib	skin:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:58003774-58003824	PFSK-1	brain:	n/a
2	chr12:58003774-58003824	MCF-7	breast:	n/a
3	chr12:58003774-58003824	SK-N-MC	brain:	n/a
4	chr12:58003774-58003824	Hepatocyte	liver:	n/a
5	chr12:58003774-58003824	K562	blood:	n/a
6	chr12:58003774-58003824	SK-N-SH_RA	brain:	n/a
7	chr12:58003774-58003824	NHBE	bronchial:	n/a
8	chr12:58003774-58003824	HRCEpiC	kidney:	n/a
9	chr12:58003774-58003824	AoSMC	blood vessel:	n/a
10	chr12:58003774-58003824	HPAEpiC	pulmonary alveolar:	n/a
11	chr12:58003774-58003824	HRE	kidney:	n/a
12	chr12:58003774-58003824	HAEpiC	amniotic membrane:	n/a
13	chr12:58003774-58003824	MCF10A-Er-Src	breast:	n/a
14	chr12:58003774-58003824	HNPCEpiC	eye:	n/a
15	chr12:58003774-58003824	NH-A	brain:	n/a
16	chr12:58003774-58003824	SKMC	muscle:	n/a
17	chr12:58003774-58003824	SAEC	small airway:	n/a
18	chr12:58003774-58003824	RPTEC	kidney:	n/a
19	chr12:58003774-58003824	NHDF-neo	bronchial:	n/a
20	chr12:58003774-58003824	Hela-S3	cervix:	n/a
21	chr12:58003774-58003824	H1-hESC	embryonic stem cell:	embryo
22	chr12:58003774-58003824	AG09319	gingival:	n/a
23	chr12:58003774-58003824	ovcar-3	ovarian:	n/a
24	chr12:58003774-58003824	A549	lung:	n/a
25	chr12:58003774-58003824	SK-N-SH	brain:	n/a
26	chr12:58003774-58003824	GM06990	blood:	n/a
27	chr12:58003774-58003824	GM12891	blood:	n/a
28	chr12:58003774-58003824	AG09309	skin:	n/a
29	chr12:58003774-58003824	PANC-1	pancreas:	n/a
30	chr12:58003774-58003824	GM19239	blood:	n/a
31	chr12:58003774-58003824	HL-60	blood:	n/a
32	chr12:58003774-58003824	BJ	skin:	n/a
33	chr12:58003774-58003824	Caco-2	colon:	n/a
34	chr12:58003774-58003824	HMEC	breast:	n/a
35	chr12:58003774-58003824	CMK	blood:	n/a
36	chr12:58003774-58003824	GM12892	blood:	n/a
37	chr12:58003774-58003824	HCM	heart:	n/a
38	chr12:58003774-58003824	T-47D	breast:	n/a
39	chr12:58003774-58003824	AG10803	skin:	n/a
40	chr12:58003774-58003824	IMR90	lung:	fetal
41	chr12:58003774-58003824	GM12878	blood:	n/a
42	chr12:58003774-58003824	U87	brain:	n/a
43	chr12:58003774-58003824	HEEpiC	esophagus:	n/a
44	chr12:58003774-58003824	BE2_C	brain:	n/a
45	chr12:58003774-58003824	AG04449	skin:	fetal
46	chr12:58003774-58003824	NB4	blood:	n/a
47	chr12:58003774-58003824	LNCaP	prostate:	n/a
48	chr12:58003774-58003824	ProgFib	skin:	n/a
49	chr12:58003774-58003824	HIPEpiC	eye:	n/a
50	chr12:58003774-58003824	HCPEpiC	choroid plexus:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57912257..57915408-chr12:58000825..58006358,4	K562	blood:
2	chr12:57930705..57935401-chr12:58001977..58005950,4	K562	blood:
3	chr12:57911699..57918406-chr12:58000825..58010019,18	K562	blood:
4	chr12:58002964..58008004-chr12:58117447..58122099,5	MCF-7	breast:
5	chr12:57939583..57941703-chr12:58002111..58004794,2	K562	blood:
6	chr12:58003234..58004876-chr12:58145695..58148256,2	K562	blood:
7	chr12:57634341..57637032-chr12:58003121..58004920,2	K562	blood:
8	chr12:58003448..58005159-chr12:58329612..58331307,2	K562	blood:

No data

Variant related genes	Relation type
ARHGEF25	TF binding region
ARHGEF25	CpG island
ENSG00000185633	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000257698	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000208028	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs57624896	0.90[AFR][1000 genomes]
rs57989706	1.00[AFR][1000 genomes]
rs58060255	0.81[AFR][1000 genomes]
rs59166749	0.91[AFR][1000 genomes]
rs59193499	0.90[AFR][1000 genomes]
rs73335926	0.90[AFR][1000 genomes]
rs73335930	0.90[AFR][1000 genomes]
rs73335931	0.90[AFR][1000 genomes]
rs73338203	0.90[AFR][1000 genomes]
rs73346063	0.81[AFR][1000 genomes]
rs73346089	1.00[AFR][1000 genomes]
rs73347951	0.90[AFR][1000 genomes]
rs73349943	0.90[AFR][1000 genomes]
rs73351685	0.90[AFR][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	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57999400-58004000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:57999400-58004000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:57999400-58004800	Weak transcription	Gastric	stomach
4	chr12:57999600-58003800	Weak transcription	Aorta	Aorta
5	chr12:57999600-58004000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:57999600-58004200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr12:57999600-58004200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr12:57999600-58004200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr12:57999600-58004200	Weak transcription	NH-A	brain
10	chr12:57999600-58004200	Weak transcription	NHLF	lung
11	chr12:57999600-58004600	Weak transcription	GM12878-XiMat	blood
12	chr12:57999800-58003800	Weak transcription	Colonic Mucosa	Colon
13	chr12:57999800-58003800	Weak transcription	Right Atrium	heart
14	chr12:57999800-58004000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:57999800-58004000	Weak transcription	NHDF-Ad	bronchial
16	chr12:57999800-58004000	Weak transcription	Osteobl	bone
17	chr12:57999800-58004200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:57999800-58004200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:57999800-58004200	Weak transcription	Pancreas	Pancrea
20	chr12:57999800-58004600	Weak transcription	A549	lung
21	chr12:57999800-58004800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:57999800-58004800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:58000000-58003800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:58000000-58003800	Weak transcription	Fetal Brain Male	brain
25	chr12:58000000-58004200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:58000000-58004200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:58000600-58004000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr12:58001600-58004200	Weak transcription	Lung	lung
29	chr12:58001600-58004600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:58001800-58004200	Weak transcription	Brain Substantia Nigra	brain
31	chr12:58002600-58003800	Weak transcription	Esophagus	oesophagus
32	chr12:58002800-58003800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:58002800-58004400	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr12:58002800-58004800	Enhancers	K562	blood
35	chr12:58003000-58003800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:58003000-58003800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:58003000-58003800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr12:58003000-58003800	Flanking Active TSS	Rectal Smooth Muscle	rectum
39	chr12:58003000-58004000	Enhancers	Fetal Heart	heart
40	chr12:58003000-58004200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr12:58003000-58004400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr12:58003000-58005800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
43	chr12:58003200-58003800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:58003200-58003800	Weak transcription	Left Ventricle	heart
45	chr12:58003200-58004200	Weak transcription	Primary T cells from cord blood	blood
46	chr12:58003200-58004200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:58003200-58004400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr12:58003200-58004600	Weak transcription	Spleen	Spleen
49	chr12:58003200-58004800	Bivalent Enhancer	Fetal Thymus	thymus
50	chr12:58003200-58005000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle

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