Variant report

Variant	rs13093914
Chromosome Location	chr3:46931387-46931388
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr3:46930883-46931531	K562	blood:	n/a	n/a
2	SPI1	chr3:46931283-46931447	K562	blood:	n/a	n/a
3	NFIC	chr3:46931073-46931742	ECC-1	luminal epithelium:	n/a	chr3:46931376-46931393 chr3:46931377-46931393
4	NFIC	chr3:46931119-46931662	ECC-1	luminal epithelium:	n/a	chr3:46931376-46931393 chr3:46931377-46931393
5	ZNF263	chr3:46930942-46931943	HEK293-T-REx	kidney:	n/a	n/a
6	ELF1	chr3:46931187-46931564	K562	blood:	n/a	n/a
7	CTCF	chr3:46931300-46931450	WERI-Rb-1	eye:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:46931381-46931431	SK-N-MC	brain:	n/a
2	chr3:46931381-46931431	MCF10A-Er-Src	breast:	n/a
3	chr3:46931381-46931431	MCF-7	breast:	n/a
4	chr3:46931381-46931431	CMK	blood:	n/a
5	chr3:46931381-46931431	Jurkat	blood:	n/a
6	chr3:46931381-46931431	IMR90	lung:	fetal
7	chr3:46931381-46931431	AG09319	gingival:	n/a
8	chr3:46931381-46931431	ECC-1	luminal epithelium:	n/a
9	chr3:46931381-46931431	GM12892	blood:	n/a
10	chr3:46931381-46931431	SK-N-SH_RA	brain:	n/a
11	chr3:46931381-46931431	HCM	heart:	n/a
12	chr3:46931381-46931431	HIPEpiC	eye:	n/a
13	chr3:46931381-46931431	HCPEpiC	choroid plexus:	n/a
14	chr3:46931381-46931431	PANC-1	pancreas:	n/a
15	chr3:46931381-46931431	Hepatocyte	liver:	n/a
16	chr3:46931381-46931431	GM12891	blood:	n/a
17	chr3:46931381-46931431	SK-N-SH	brain:	n/a
18	chr3:46931381-46931431	AG09309	skin:	n/a
19	chr3:46931381-46931431	HL-60	blood:	n/a
20	chr3:46931381-46931431	T-47D	breast:	n/a
21	chr3:46931381-46931431	HepG2	liver:	n/a
22	chr3:46931381-46931431	HRCEpiC	kidney:	n/a
23	chr3:46931381-46931431	GM12878	blood:	n/a
24	chr3:46931381-46931431	AG04449	skin:	fetal
25	chr3:46931381-46931431	AoSMC	blood vessel:	n/a
26	chr3:46931381-46931431	HEK293	kidney:	embryo
27	chr3:46931381-46931431	AG10803	skin:	n/a
28	chr3:46931381-46931431	BE2_C	brain:	n/a
29	chr3:46931381-46931431	ovcar-3	ovarian:	n/a
30	chr3:46931381-46931431	HRPEpiC	eye:	n/a
31	chr3:46931381-46931431	NHDF-neo	bronchial:	n/a
32	chr3:46931381-46931431	SKMC	muscle:	n/a
33	chr3:46931381-46931431	BJ	skin:	n/a
34	chr3:46931381-46931431	NB4	blood:	n/a
35	chr3:46931381-46931431	A549	lung:	n/a
36	chr3:46931381-46931431	HPAEpiC	pulmonary alveolar:	n/a
37	chr3:46931381-46931431	GM06990	blood:	n/a
38	chr3:46931381-46931431	PFSK-1	brain:	n/a
39	chr3:46931381-46931431	NH-A	brain:	n/a
40	chr3:46931381-46931431	HCF	heart:	n/a
41	chr3:46931381-46931431	Caco-2	colon:	n/a
42	chr3:46931381-46931431	GM19239	blood:	n/a
43	chr3:46931381-46931431	HUVEC	blood vessel:	n/a
44	chr3:46931381-46931431	U87	brain:	n/a
45	chr3:46931381-46931431	HRE	kidney:	n/a
46	chr3:46931381-46931431	SAEC	small airway:	n/a
47	chr3:46931381-46931431	HMEC	breast:	n/a
48	chr3:46931381-46931431	RPTEC	kidney:	n/a
49	chr3:46931381-46931431	H1-hESC	embryonic stem cell:	embryo
50	chr3:46931381-46931431	NHBE	bronchial:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:46923987..46927246-chr3:46931255..46933897,4	K562	blood:
2	chr3:46929621..46931545-chr3:47041151..47042840,2	K562	blood:
3	chr3:46929163..46931629-chr3:46932279..46935009,2	K562	blood:

No data

Variant related genes	Relation type
PTH1R	TF binding region
ENSG00000268537	TF binding region
ENSG00000268537	CpG island
PTH1R	CpG island
ENSG00000160801	Chromatin interaction
ENSG00000160796	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13083011	0.88[EUR][1000 genomes]
rs1869873	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34188610	0.88[EUR][1000 genomes]
rs71327101	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7651753	0.88[EUR][1000 genomes]
rs936183	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1003979	chr3:46853374-46943854	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv590206	chr3:46873957-46935527	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv876753	chr3:46884552-46957298	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46925200-46933000	Weak transcription	Pancreas	Pancrea
2	chr3:46925800-46933000	Weak transcription	Brain Angular Gyrus	brain
3	chr3:46926000-46933400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:46926600-46933000	Weak transcription	Left Ventricle	heart
5	chr3:46926600-46933200	Weak transcription	Brain Anterior Caudate	brain
6	chr3:46926600-46933400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:46929000-46931800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
8	chr3:46929200-46931400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:46929400-46933000	Enhancers	Fetal Lung	lung
10	chr3:46930000-46931800	Enhancers	Right Atrium	heart
11	chr3:46930200-46931400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:46930200-46931600	Enhancers	Adipose Nuclei	Adipose
13	chr3:46930200-46931800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:46930400-46931800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
15	chr3:46930400-46932000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr3:46930400-46932000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr3:46930400-46932000	Enhancers	Lung	lung
18	chr3:46930400-46932200	Enhancers	Right Ventricle	heart
19	chr3:46930400-46933600	Enhancers	Ovary	ovary
20	chr3:46930400-46933800	Enhancers	Spleen	Spleen
21	chr3:46930600-46931600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:46930600-46932000	Enhancers	Stomach Smooth Muscle	stomach
23	chr3:46930600-46933800	Bivalent Enhancer	Placenta	Placenta
24	chr3:46930800-46931600	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr3:46930800-46931800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
26	chr3:46930800-46932800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:46930800-46933000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:46931000-46931400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:46931000-46931800	Enhancers	Fetal Heart	heart
30	chr3:46931000-46932000	Enhancers	Fetal Intestine Large	intestine
31	chr3:46931000-46933200	Enhancers	Fetal Kidney	kidney
32	chr3:46931200-46931400	Enhancers	Esophagus	oesophagus
33	chr3:46931200-46931600	Enhancers	HSMMtube	muscle
34	chr3:46931200-46931800	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr3:46931200-46931800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:46931200-46931800	Bivalent Enhancer	Fetal Intestine Small	intestine
37	chr3:46931200-46931800	Bivalent Enhancer	Fetal Thymus	thymus
38	chr3:46931200-46932000	Enhancers	Primary hematopoietic stem cells	blood
39	chr3:46931200-46932000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:46931200-46932000	Bivalent Enhancer	Fetal Stomach	stomach
41	chr3:46931200-46932000	Enhancers	K562	blood
42	chr3:46931200-46932800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:46931200-46933400	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links