Variant report

Variant	rs2899830
Chromosome Location	chr14:35593599-35593600
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr14:35593387-35593790	GM12878	blood:	n/a	n/a
2	RUNX3	chr14:35593447-35593694	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr14:35589827..35591407-chr14:35592886..35594751,2	K562	blood:
2	chr14:35341168..35344675-chr14:35590606..35593872,6	MCF-7	breast:
3	chr14:35450019..35452754-chr14:35591061..35594828,4	K562	blood:
4	chr14:35591658..35595888-chr14:35872338..35875561,5	K562	blood:
5	chr14:35450042..35454830-chr14:35589505..35593708,8	K562	blood:
6	chr14:35592944..35595456-chr14:35809160..35811582,2	K562	blood:
7	chr14:35589196..35594400-chr14:35871301..35877730,13	MCF-7	breast:
8	chr14:35513731..35517214-chr14:35589119..35593617,5	MCF-7	breast:
9	chr14:35589240..35593864-chr14:35869008..35876501,20	MCF-7	breast:
10	chr14:35512802..35518057-chr14:35589980..35593805,9	MCF-7	breast:

No data

Variant related genes	Relation type
PPP2R3C	TF binding region
ENSG00000258738	Chromatin interaction
ENSG00000100890	Chromatin interaction
ENSG00000100883	Chromatin interaction
ENSG00000258704	Chromatin interaction
ENSG00000151327	Chromatin interaction
ENSG00000092020	Chromatin interaction
ENSG00000100906	Chromatin interaction
ENSG00000198604	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1056879	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11845837	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11851907	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12879871	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17103005	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17103034	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1807161	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1961195	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2143950	0.82[ASN][1000 genomes]
rs2179890	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2236167	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2415260	0.82[ASN][1000 genomes]
rs2415261	0.83[ASN][1000 genomes]
rs2415262	0.83[ASN][1000 genomes]
rs28365850	0.84[ASN][1000 genomes]
rs28397987	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28765972	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4456414	0.84[ASN][1000 genomes]
rs55977244	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56027918	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57075379	0.81[ASN][1000 genomes]
rs57473972	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58770366	0.85[ASN][1000 genomes]
rs7142489	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7144423	0.82[ASN][1000 genomes]
rs7146682	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7153660	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7158416	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7158634	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72664807	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72680650	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8005406	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8006583	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8006884	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8006935	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8014091	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8019351	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs941653	0.84[ASN][1000 genomes]
rs9671773	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9672061	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949617	chr14:35379923-35825436	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv1043470	chr14:35398522-35754029	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv542031	chr14:35398522-35754029	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv564264	chr14:35482797-35732369	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv901615	chr14:35485748-35630175	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv870305	chr14:35488290-35852349	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv1052800	chr14:35509858-35607117	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1044515	chr14:35510785-35756317	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv564265	chr14:35512335-35624831	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers 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 miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv1046992	chr14:35527239-35724227	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv1051274	chr14:35529529-35724227	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv1048823	chr14:35537281-35724892	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv542032	chr14:35537281-35724892	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv1040540	chr14:35537481-35724753	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv542033	chr14:35537481-35724753	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv1042625	chr14:35546094-35680358	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
17	nsv1050123	chr14:35546114-35724892	Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
18	nsv542034	chr14:35546114-35724892	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
19	nsv1050700	chr14:35548276-35639084	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
20	nsv1043692	chr14:35548276-35720016	Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
21	nsv1053604	chr14:35548276-35825805	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
22	nsv542035	chr14:35563220-35607117	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
23	nsv1047992	chr14:35563220-35639084	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
24	nsv1052392	chr14:35563220-35893309	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
25	nsv542036	chr14:35563220-35893309	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
26	nsv1053978	chr14:35571762-35639084	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
27	nsv534182	chr14:35579022-35620232	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2899830	PPP2R3C	cis	Whole Blood	GTEx
rs2899830	PPP2R3C	cis	multi-tissue	Pritchard
rs2899830	PPP2R3C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35589800-35595000	Active TSS	K562	blood
2	chr14:35592200-35600000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:35592400-35603000	Weak transcription	Ovary	ovary
4	chr14:35592600-35599800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr14:35592600-35602800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:35592600-35602800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr14:35592600-35602800	Weak transcription	Spleen	Spleen
8	chr14:35592600-35603000	Weak transcription	Esophagus	oesophagus
9	chr14:35592600-35603000	Weak transcription	Gastric	stomach
10	chr14:35592600-35603200	Weak transcription	Left Ventricle	heart
11	chr14:35592600-35603200	Weak transcription	Pancreas	Pancrea
12	chr14:35592600-35603400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr14:35592600-35625200	Weak transcription	Small Intestine	intestine
14	chr14:35592800-35593800	Enhancers	Liver	Liver
15	chr14:35592800-35603200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr14:35592800-35611000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr14:35593000-35593800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr14:35593000-35594000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr14:35593000-35594000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr14:35593000-35594000	Enhancers	Fetal Intestine Small	intestine
21	chr14:35593000-35594200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr14:35593000-35594200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr14:35593000-35594200	Weak transcription	Colonic Mucosa	Colon
24	chr14:35593000-35594800	Enhancers	Primary B cells from cord blood	blood
25	chr14:35593000-35595200	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr14:35593000-35595200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr14:35593000-35595400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr14:35593000-35595800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr14:35593000-35596200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr14:35593000-35596800	Weak transcription	HSMM	muscle
31	chr14:35593000-35598000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr14:35593000-35601000	Weak transcription	Psoas Muscle	Psoas
33	chr14:35593000-35601400	Weak transcription	Brain Germinal Matrix	brain
34	chr14:35593000-35601400	Weak transcription	Fetal Muscle Leg	muscle
35	chr14:35593000-35602800	Weak transcription	Adipose Nuclei	Adipose
36	chr14:35593000-35602800	Weak transcription	Placenta	Placenta
37	chr14:35593000-35602800	Weak transcription	Lung	lung
38	chr14:35593000-35602800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr14:35593000-35603400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr14:35593000-35603400	Weak transcription	Right Atrium	heart
41	chr14:35593000-35603800	Weak transcription	Brain Anterior Caudate	brain
42	chr14:35593000-35603800	Weak transcription	Right Ventricle	heart
43	chr14:35593000-35605200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr14:35593000-35610200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr14:35593000-35613400	Weak transcription	Stomach Mucosa	stomach
46	chr14:35593000-35638200	Weak transcription	Fetal Brain Male	brain
47	chr14:35593000-35660400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr14:35593200-35594000	Enhancers	Primary hematopoietic stem cells	blood
49	chr14:35593200-35594000	Enhancers	HUVEC	blood vessel
50	chr14:35593200-35594200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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