Variant report

Variant	rs3813008
Chromosome Location	chr16:31497881-31497882
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:31497771-31497936	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:31497102-31498095	K562	blood:	n/a	n/a
3	POLR2A	chr16:31495945-31497999	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:31494997..31499043-chr16:31517756..31521950,4	K562	blood:
2	chr16:31493200..31498370-chr16:31536887..31540209,4	K562	blood:
3	chr16:31497480..31508766-chr16:31514543..31521176,19	MCF-7	breast:
4	chr16:31482515..31485868-chr16:31497342..31499348,3	MCF-7	breast:
5	chr16:31494438..31500083-chr16:31500912..31506203,9	K562	blood:
6	chr16:31497080..31498876-chr16:31503368..31505662,2	K562	blood:
7	chr16:31468059..31475073-chr16:31494279..31502185,17	MCF-7	breast:
8	chr16:31469520..31471789-chr16:31495046..31498029,3	MCF-7	breast:

No data

Variant related genes	Relation type
SLC5A2	TF binding region
ENSG00000140688	Chromatin interaction
ENSG00000260625	Chromatin interaction
ENSG00000260267	Chromatin interaction
ENSG00000140691	Chromatin interaction
ENSG00000169877	Chromatin interaction
ENSG00000140682	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11866003	0.95[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13338939	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs17677	0.95[CEU][hapmap]
rs3116149	0.98[ASN][1000 genomes]
rs4296276	0.81[AMR][1000 genomes]
rs4411513	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4499252	0.95[CEU][hapmap];1.00[MEX][hapmap]
rs4553646	0.95[CEU][hapmap];1.00[MEX][hapmap]
rs4889545	0.95[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs56060924	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59813627	0.81[AMR][1000 genomes]
rs60075107	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62053184	0.81[AMR][1000 genomes]
rs7202020	0.95[CEU][hapmap];0.86[MEX][hapmap]
rs8047112	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9921597	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
2	nsv833194	chr16:31358179-31528545	Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
4	nsv905748	chr16:31427678-31559220	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
5	nsv905749	chr16:31427678-31565597	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	96 gene(s)	inside rSNPs	diseases
6	nsv905750	chr16:31427678-31587662	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
7	nsv905752	chr16:31436932-31565597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases
8	nsv905753	chr16:31436932-31587662	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
9	nsv905754	chr16:31451699-31565597	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
10	nsv482193	chr16:31494439-31502091	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
11	nsv1060240	chr16:31495873-31581450	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3813008	CD2BP2	cis	cerebellum	SCAN
rs3813008	COX6A2	cis	parietal	SCAN
rs3813008	NUPR1	cis	cerebellum	SCAN
rs3813008	PRSS53	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31489400-31498600	Weak transcription	Esophagus	oesophagus
2	chr16:31489400-31498600	Weak transcription	Ovary	ovary
3	chr16:31489600-31498600	Weak transcription	Left Ventricle	heart
4	chr16:31489600-31498800	Weak transcription	Aorta	Aorta
5	chr16:31490000-31498400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr16:31490000-31498600	Weak transcription	Liver	Liver
7	chr16:31490600-31498600	Weak transcription	Pancreas	Pancrea
8	chr16:31492400-31498600	Weak transcription	Right Atrium	heart
9	chr16:31492600-31498600	Weak transcription	Spleen	Spleen
10	chr16:31495800-31498200	Enhancers	Colonic Mucosa	Colon
11	chr16:31495800-31498400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr16:31495800-31498400	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr16:31496200-31498400	Weak transcription	HMEC	breast
14	chr16:31496200-31503600	Weak transcription	K562	blood
15	chr16:31496400-31498600	Weak transcription	Fetal Heart	heart
16	chr16:31496400-31498600	Weak transcription	Right Ventricle	heart
17	chr16:31496400-31498800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr16:31496600-31498200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr16:31496600-31498400	Weak transcription	Fetal Lung	lung
20	chr16:31496600-31498400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr16:31496600-31498600	Weak transcription	Gastric	stomach
22	chr16:31496600-31498600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr16:31496600-31498600	Weak transcription	A549	lung
24	chr16:31496800-31498400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr16:31497000-31498600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr16:31497000-31501200	Weak transcription	HepG2	liver
27	chr16:31497000-31501800	Weak transcription	Dnd41	blood
28	chr16:31497400-31498000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr16:31497400-31498600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr16:31497600-31498000	Flanking Active TSS	Fetal Intestine Large	intestine
31	chr16:31497600-31498000	Flanking Active TSS	Fetal Intestine Small	intestine
32	chr16:31497600-31498400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr16:31497600-31498600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr16:31497600-31498600	Weak transcription	Lung	lung
35	chr16:31497800-31498000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
36	chr16:31497800-31498000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
37	chr16:31497800-31498200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr16:31497800-31498400	Enhancers	Primary hematopoietic stem cells	blood
39	chr16:31497800-31498400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr16:31497800-31498600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr16:31497800-31498600	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr16:31497800-31498600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr16:31497800-31498600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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