Variant report

Variant	rs17128120
Chromosome Location	chr14:55474598-55474599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55474408..55478459-chr14:55493227..55495809,4	K562	blood:

Variant related genes	Relation type
ENSG00000198554	Chromatin interaction
ENSG00000180008	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1002054	0.87[JPT][hapmap]
rs10139354	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10140164	1.00[ASW][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs10145268	0.87[JPT][hapmap]
rs10148100	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10150110	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1107960	0.86[CEU][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11158028	0.86[JPT][hapmap]
rs11621165	0.86[JPT][hapmap]
rs11846514	0.91[ASN][1000 genomes]
rs1187876	0.85[JPT][hapmap]
rs1187877	0.87[JPT][hapmap]
rs1187883	0.93[JPT][hapmap]
rs1201378	0.87[JPT][hapmap]
rs1209087	0.87[JPT][hapmap]
rs13379159	0.87[JPT][hapmap]
rs17832269	0.86[ASN][1000 genomes]
rs17832311	0.87[JPT][hapmap]
rs2183081	0.80[CEU][hapmap];0.84[TSI][hapmap]
rs2183085	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2251366	0.87[JPT][hapmap]
rs2840268	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28446981	0.96[ASN][1000 genomes]
rs28481699	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28693954	0.96[ASN][1000 genomes]
rs2878172	0.87[ASW][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap]
rs2878174	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs34988865	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742564	0.87[JPT][hapmap]
rs3759664	0.86[JPT][hapmap]
rs3783643	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3783644	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3783646	0.91[ASN][1000 genomes]
rs4325453	0.90[ASN][1000 genomes]
rs4335711	0.87[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs56164809	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56206440	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56335168	0.85[ASN][1000 genomes]
rs57667631	0.84[ASN][1000 genomes]
rs57922954	0.85[ASN][1000 genomes]
rs58055971	0.85[ASN][1000 genomes]
rs59323730	0.89[ASN][1000 genomes]
rs60028867	0.91[ASN][1000 genomes]
rs6572993	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6572994	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6572997	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6572999	0.87[JPT][hapmap]
rs66769866	0.91[ASN][1000 genomes]
rs66820631	0.84[ASN][1000 genomes]
rs67395322	0.95[ASN][1000 genomes]
rs67571433	0.91[ASN][1000 genomes]
rs68065548	0.85[ASN][1000 genomes]
rs7144652	0.87[JPT][hapmap]
rs7146285	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7147286	0.84[CEU][hapmap]
rs7151670	0.91[ASN][1000 genomes]
rs7153937	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7157085	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7159232	0.86[ASN][1000 genomes]
rs7159933	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72715573	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8005399	0.87[JPT][hapmap]
rs8005471	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8006977	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8007267	0.86[JPT][hapmap]
rs8009997	0.86[ASN][1000 genomes]
rs8011446	0.86[ASN][1000 genomes]
rs8012152	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8012156	0.87[JPT][hapmap]
rs8013521	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8015172	0.85[ASN][1000 genomes]
rs8018800	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8019220	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8019390	0.93[JPT][hapmap]
rs8020545	0.93[JPT][hapmap]
rs8021303	0.87[ASN][1000 genomes]
rs8021370	0.83[ASN][1000 genomes]
rs8022049	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8022453	0.86[JPT][hapmap]
rs8023187	0.92[JPT][hapmap]
rs9285583	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9323275	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs943914	0.93[ASN][1000 genomes]
rs9805952	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9806049	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932970	chr14:55326559-55532749	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv976342	chr14:55468718-55474623	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17128120	FBXO34	cis	cerebellum	SCAN
rs17128120	ATG14	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55411000-55477000	Weak transcription	Left Ventricle	heart
2	chr14:55418600-55492200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:55419800-55480400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr14:55421800-55481400	Weak transcription	Placenta	Placenta
5	chr14:55421800-55492800	Weak transcription	Aorta	Aorta
6	chr14:55422400-55492400	Weak transcription	Fetal Kidney	kidney
7	chr14:55424200-55476800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr14:55427200-55477400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr14:55429000-55492400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr14:55429600-55479000	Weak transcription	Fetal Brain Female	brain
11	chr14:55430400-55484000	Weak transcription	Lung	lung
12	chr14:55434000-55492800	Weak transcription	Primary B cells from cord blood	blood
13	chr14:55434200-55486800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr14:55437600-55483600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:55438600-55490200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr14:55439400-55485600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr14:55439400-55490200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr14:55439800-55479400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr14:55442200-55492800	Weak transcription	Fetal Intestine Large	intestine
20	chr14:55442600-55480600	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr14:55443200-55481200	Weak transcription	Pancreas	Pancrea
22	chr14:55443400-55492200	Weak transcription	NHLF	lung
23	chr14:55444200-55480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr14:55447800-55484600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr14:55450000-55479800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr14:55454200-55492400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr14:55454800-55478800	Weak transcription	Fetal Brain Male	brain
28	chr14:55454800-55479000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr14:55455800-55479600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr14:55455800-55486600	Weak transcription	HepG2	liver
31	chr14:55458400-55477000	Weak transcription	Fetal Lung	lung
32	chr14:55458400-55492200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr14:55458400-55492200	Weak transcription	NH-A	brain
34	chr14:55461200-55485200	Strong transcription	Dnd41	blood
35	chr14:55461600-55483200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr14:55464400-55486800	Weak transcription	Fetal Heart	heart
37	chr14:55465200-55478200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr14:55465200-55480400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr14:55467800-55474600	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr14:55467800-55486800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr14:55468200-55477800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr14:55468600-55478000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr14:55468600-55479200	Weak transcription	HSMM	muscle
44	chr14:55468600-55492400	Weak transcription	Osteobl	bone
45	chr14:55468800-55479400	Weak transcription	K562	blood
46	chr14:55468800-55481600	Weak transcription	HMEC	breast
47	chr14:55468800-55492200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr14:55469800-55475200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr14:55470000-55479800	Weak transcription	Gastric	stomach
50	chr14:55471000-55480600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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