Variant report

Variant	rs31920
Chromosome Location	chr5:14667484-14667485
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr5:14663672-14668468	Hela-S3	cervix:	n/a	n/a
2	WRNIP1	chr5:14667322-14668730	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:14663431..14670152-chr5:14672054..14680588,17	K562	blood:
2	chr5:14664510..14666859-chr5:14666995..14670129,4	MCF-7	breast:
3	chr5:14666421..14668371-chr5:14694301..14697182,2	K562	blood:
4	chr5:14666399..14668895-chr5:14676273..14677945,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261360	TF binding region
ENSG00000261360	Chromatin interaction
ENSG00000154124	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10062487	0.86[EUR][1000 genomes]
rs10078335	0.88[EUR][1000 genomes]
rs13189930	0.87[JPT][hapmap]
rs149181	0.82[ASN][1000 genomes]
rs149493	0.84[ASN][1000 genomes]
rs149617	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs152788	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs153829	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs153830	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs166127	0.88[ASN][1000 genomes]
rs183681	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1875513	1.00[JPT][hapmap]
rs2455402	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs250435	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs250439	0.84[ASN][1000 genomes]
rs250440	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs250862	0.86[ASN][1000 genomes]
rs251496	0.87[ASN][1000 genomes]
rs258290	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs258374	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs25945	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs25951	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs25952	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs25983	0.87[JPT][hapmap]
rs25986	0.82[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs25987	0.82[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs25988	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs25992	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26307	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs27356	0.87[JPT][hapmap]
rs27882	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27911	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28004	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs31919	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs31921	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs31922	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs31923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs31924	0.81[ASN][1000 genomes]
rs31925	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs31926	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs31928	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs31929	0.90[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs31930	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs31968	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3866215	0.85[JPT][hapmap]
rs40578	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42358	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs42410	0.98[ASN][1000 genomes]
rs42681	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs456180	0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs459467	0.87[ASN][1000 genomes]
rs466880	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4702043	1.00[JPT][hapmap]
rs6554856	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6872954	1.00[JPT][hapmap]
rs73048831	0.86[EUR][1000 genomes]
rs73048837	0.84[EUR][1000 genomes]
rs73048838	0.80[EUR][1000 genomes]
rs745328	0.93[JPT][hapmap]
rs95492	0.90[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv830211	chr5:14474675-14675776	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14665600-14676600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:14665800-14668000	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr5:14665800-14668600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr5:14666000-14668800	Enhancers	Small Intestine	intestine
5	chr5:14666200-14667600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr5:14666200-14667800	Enhancers	Primary B cells from peripheral blood	blood
7	chr5:14666200-14668400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr5:14666200-14668800	Enhancers	Fetal Heart	heart
9	chr5:14666200-14669000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr5:14666200-14672200	Weak transcription	Aorta	Aorta
11	chr5:14666400-14667600	Enhancers	Fetal Intestine Small	intestine
12	chr5:14666400-14667600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr5:14666400-14668000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:14666400-14668400	Enhancers	Colon Smooth Muscle	Colon
15	chr5:14666400-14669200	Enhancers	Fetal Intestine Large	intestine
16	chr5:14666400-14669800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:14666400-14671200	Weak transcription	Brain Angular Gyrus	brain
18	chr5:14666400-14672200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:14666400-14673200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:14666400-14673200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:14666400-14674200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr5:14666400-14675600	Weak transcription	Placenta	Placenta
23	chr5:14666400-14678200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:14666400-14681600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:14666400-14688200	Weak transcription	Ovary	ovary
26	chr5:14666600-14667800	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr5:14666600-14668000	Weak transcription	Colonic Mucosa	Colon
28	chr5:14666600-14668400	Transcr. at gene 5' and 3'	Hela-S3	cervix
29	chr5:14666600-14669600	Weak transcription	NH-A	brain
30	chr5:14666600-14671000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr5:14666600-14672000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:14666600-14672200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:14666600-14688200	Weak transcription	Brain Germinal Matrix	brain
34	chr5:14666800-14667600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:14666800-14667600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr5:14666800-14667600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr5:14666800-14667600	Weak transcription	Fetal Muscle Leg	muscle
38	chr5:14666800-14667600	Enhancers	HepG2	liver
39	chr5:14666800-14668000	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr5:14666800-14668000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:14666800-14668000	Weak transcription	Psoas Muscle	Psoas
42	chr5:14666800-14668200	Enhancers	Primary T cells fromperipheralblood	blood
43	chr5:14666800-14668200	Weak transcription	Right Atrium	heart
44	chr5:14666800-14668800	Enhancers	Adipose Nuclei	Adipose
45	chr5:14666800-14668800	Genic enhancers	K562	blood
46	chr5:14666800-14669000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr5:14666800-14669000	Enhancers	Liver	Liver
48	chr5:14666800-14669200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr5:14666800-14670000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:14666800-14671200	Weak transcription	Rectal Smooth Muscle	rectum

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