Variant report

Variant	rs2773269
Chromosome Location	chr13:52380306-52380307
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr13:52380121-52380374	H1-hESC	embryonic stem cell:	n/a	n/a
2	CBX3	chr13:52380029-52380443	K562	blood:	n/a	n/a
3	RCOR1	chr13:52380112-52380418	K562	blood:	n/a	n/a
4	POLR2A	chr13:52376283-52380704	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr13:52375841-52380503	MCF10A-Er-Src	breast:	n/a	n/a
6	ZNF143	chr13:52380115-52380357	K562	blood:	n/a	n/a
7	RCOR1	chr13:52380166-52380348	HepG2	liver:	n/a	n/a
8	RCOR1	chr13:52380124-52380448	K562	blood:	n/a	n/a
9	RCOR1	chr13:52379550-52380413	IMR90	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:52379385..52381613-chr13:52498581..52500814,2	K562	blood:
2	chr13:52024232..52029374-chr13:52366504..52381003,28	MCF-7	breast:
3	chr13:52022728..52028464-chr13:52376436..52381467,17	K562	blood:
4	chr13:52023047..52029598-chr13:52376243..52380914,21	K562	blood:
5	chr13:52380223..52382865-chr13:52393568..52395438,2	K562	blood:
6	chr13:52362645..52365632-chr13:52377625..52381040,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDFY2-1	chr13:52378295-52387482	NONHSAT033952

No data

Variant related genes	Relation type
DHRS12	TF binding region
ENSG00000102796	Chromatin interaction
ENSG00000224892	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2734	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760302	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2760303	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2760304	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2760305	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2773267	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs512948	1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs518210	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs541434	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs732004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv1840020	chr13:52345838-52388765	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2773269	FNDC3A	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52378600-52389200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr13:52378800-52385000	Weak transcription	Lung	lung
3	chr13:52379000-52380400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
4	chr13:52379000-52380600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr13:52379000-52381800	Enhancers	Fetal Heart	heart
6	chr13:52379000-52385000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:52379000-52389000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr13:52379000-52389200	Weak transcription	Ovary	ovary
9	chr13:52379200-52380400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr13:52379200-52380400	Weak transcription	HUVEC	blood vessel
11	chr13:52379200-52380600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr13:52379200-52380800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:52379200-52380800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr13:52379200-52380800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr13:52379200-52381000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr13:52379200-52381400	Enhancers	Fetal Brain Male	brain
17	chr13:52379200-52381800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr13:52379200-52385200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr13:52379200-52385600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr13:52379400-52380400	Weak transcription	Primary B cells from cord blood	blood
21	chr13:52379400-52380400	Enhancers	Fetal Brain Female	brain
22	chr13:52379400-52380400	Weak transcription	Fetal Muscle Leg	muscle
23	chr13:52379400-52380600	Weak transcription	K562	blood
24	chr13:52379400-52380800	Weak transcription	Fetal Thymus	thymus
25	chr13:52379400-52380800	Weak transcription	Left Ventricle	heart
26	chr13:52379400-52381000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr13:52379400-52381000	Enhancers	Brain Angular Gyrus	brain
28	chr13:52379400-52381000	Enhancers	Brain Anterior Caudate	brain
29	chr13:52379400-52381000	Enhancers	Brain Hippocampus Middle	brain
30	chr13:52379400-52381200	Enhancers	Brain Substantia Nigra	brain
31	chr13:52379400-52381200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr13:52379400-52381400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr13:52379400-52385000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr13:52379400-52386000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr13:52379400-52386400	Weak transcription	Hela-S3	cervix
36	chr13:52379400-52389000	Weak transcription	Placenta	Placenta
37	chr13:52379400-52389200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr13:52379600-52380400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr13:52379600-52380400	Weak transcription	Dnd41	blood
40	chr13:52379600-52380600	Weak transcription	HepG2	liver
41	chr13:52379600-52380800	Enhancers	Brain Cingulate Gyrus	brain
42	chr13:52379600-52380800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr13:52379600-52381000	Enhancers	Primary T cells fromperipheralblood	blood
44	chr13:52379600-52381000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr13:52379600-52381000	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr13:52379600-52381600	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr13:52379600-52383200	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr13:52379600-52385000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr13:52379600-52385000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr13:52379600-52385800	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links