Variant report

Variant	rs2297616
Chromosome Location	chr14:20813289-20813290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:20813254-20813320	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:20809897..20813381-chr14:20823524..20827429,6	MCF-7	breast:
2	chr14:20810118..20813648-chr14:20925784..20931556,9	MCF-7	breast:
3	chr14:20810709..20813377-chr14:20857493..20860829,3	MCF-7	breast:
4	chr14:20810041..20813384-chr14:20935508..20939122,8	MCF-7	breast:
5	chr14:20809095..20813799-chr14:21074403..21078570,5	MCF-7	breast:
6	chr14:20807684..20813516-chr14:20919958..20928823,14	K562	blood:
7	chr14:20810396..20814723-chr14:20817267..20820679,8	MCF-7	breast:
8	chr14:20811759..20814135-chr14:20820161..20822518,2	MCF-7	breast:
9	chr14:20808270..20815666-chr14:20919802..20926735,19	MCF-7	breast:
10	chr14:20809910..20813476-chr14:20877400..20881790,6	MCF-7	breast:
11	chr14:20810751..20813443-chr14:21076294..21078959,4	MCF-7	breast:

No data

Variant related genes	Relation type
RPPH1	TF binding region
ENSG00000100823	Chromatin interaction
ENSG00000129484	Chromatin interaction
ENSG00000259060	Chromatin interaction
ENSG00000165782	Chromatin interaction
ENSG00000129566	Chromatin interaction
ENSG00000198805	Chromatin interaction
ENSG00000173464	Chromatin interaction
ENSG00000092094	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10129957	0.90[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10130660	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10147163	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10148359	0.90[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10873395	0.89[CHD][hapmap]
rs11622655	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12323412	0.87[EUR][1000 genomes]
rs12323610	0.90[EUR][1000 genomes]
rs12891805	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1889362	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1889363	0.84[MEX][hapmap]
rs2104977	1.00[YRI][hapmap]
rs2318864	0.87[CHD][hapmap]
rs2700	0.84[ASW][hapmap];0.86[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3093872	1.00[LWK][hapmap]
rs3093882	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093890	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093897	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3093900	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3093902	0.88[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3093904	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3093907	0.84[ASW][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs3093909	0.89[ASN][1000 genomes]
rs3093933	0.84[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3093939	0.84[ASW][hapmap];0.90[CEU][hapmap];0.93[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs3093940	1.00[YRI][hapmap]
rs3093942	0.84[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes]
rs34848586	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3742945	0.87[CHD][hapmap]
rs4415933	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4981150	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4981153	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4981158	0.90[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4981957	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4981983	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4981998	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57101853	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58530849	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59821173	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6575124	0.90[CEU][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6575135	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7152084	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7155699	1.00[ASW][hapmap];0.80[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7159947	0.85[MEX][hapmap]
rs7161611	0.90[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8009242	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8014147	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8022565	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8022671	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs878157	0.84[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs884368	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9323870	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043923	chr14:20338742-21336425	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
2	nsv541970	chr14:20338742-21336425	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
3	nsv1037160	chr14:20517485-20901811	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
4	nsv541974	chr14:20517485-20901811	Enhancers Active TSS 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 Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
5	esv1806993	chr14:20743269-20841162	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
6	nsv534131	chr14:20757405-20886235	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1042025	chr14:20787961-20817851	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
8	esv21015	chr14:20800765-21257878	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2297616	JUB	cis	cerebellum	SCAN
rs2297616	TTC5	cis	cerebellum	SCAN
rs2297616	PARP2	cis	parietal	SCAN
rs2297616	ZNF219	cis	cerebellum	SCAN
rs2297616	NDRG2	cis	parietal	SCAN
rs2297616	RPPH1	cis	lymphoblastoid	seeQTL
rs2297616	PARP2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:20812000-20813800	Weak transcription	Lung	lung
2	chr14:20812000-20820600	Weak transcription	Spleen	Spleen
3	chr14:20812000-20822600	Weak transcription	Gastric	stomach
4	chr14:20812200-20813400	Weak transcription	Left Ventricle	heart
5	chr14:20812200-20813800	Weak transcription	Ovary	ovary
6	chr14:20812200-20815200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr14:20812200-20815200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr14:20812200-20815800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr14:20812200-20817800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr14:20812200-20822600	Weak transcription	Pancreas	Pancrea
11	chr14:20812200-20824000	Weak transcription	Aorta	Aorta
12	chr14:20812200-20825400	Weak transcription	Esophagus	oesophagus
13	chr14:20812400-20813400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr14:20812400-20815200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr14:20812400-20815200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr14:20812400-20815800	Weak transcription	Small Intestine	intestine
17	chr14:20812400-20816000	Weak transcription	Thymus	Thymus
18	chr14:20812400-20818000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr14:20812400-20820400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr14:20812400-20824400	Weak transcription	Stomach Mucosa	stomach
21	chr14:20812400-20880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr14:20812600-20813400	Weak transcription	Primary B cells from cord blood	blood
23	chr14:20812600-20813400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr14:20812600-20813400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr14:20812600-20813600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr14:20812600-20813600	Weak transcription	Adipose Nuclei	Adipose
27	chr14:20812600-20813600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr14:20812600-20813600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr14:20812600-20813800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr14:20812600-20813800	Weak transcription	Brain Angular Gyrus	brain
31	chr14:20812600-20813800	Weak transcription	Fetal Thymus	thymus
32	chr14:20812600-20814600	Weak transcription	Fetal Intestine Small	intestine
33	chr14:20812600-20814800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr14:20812600-20815000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr14:20812600-20815200	Weak transcription	Brain Substantia Nigra	brain
36	chr14:20812600-20815600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr14:20812600-20816000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr14:20812600-20816000	Weak transcription	Colon Smooth Muscle	Colon
39	chr14:20812600-20816600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr14:20812600-20817000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr14:20812600-20817200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr14:20812600-20817200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr14:20812600-20817200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr14:20812600-20817600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr14:20812600-20817800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr14:20812600-20817800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr14:20812600-20817800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr14:20812600-20818000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr14:20812600-20820200	Weak transcription	Colonic Mucosa	Colon
50	chr14:20812600-20820600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links