Variant report

Variant	rs16868771
Chromosome Location	chr5:89823684-89823685
allele	C/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	POLR2A	chr5:89821851-89826472	K562	blood:	n/a	n/a
2	POLR2A	chr5:89821783-89823769	GM12878	blood:	n/a	n/a
3	JUN	chr5:89823293-89826982	K562	blood:	n/a	chr5:89826147-89826157 chr5:89826147-89826157 chr5:89826149-89826156 chr5:89826148-89826156 chr5:89826148-89826156 chr5:89826147-89826157
4	POLR2A	chr5:89822095-89826185	IMR90	lung:	n/a	n/a
5	POLR2A	chr5:89823633-89823833	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr5:89823552-89823923	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:89823137..89824981-chr5:89966228..89967935,2	K562	blood:
2	chr5:89777835..89781277-chr5:89821033..89823702,3	K562	blood:
3	chr5:89822248..89824854-chr5:89913620..89915921,2	K562	blood:
4	chr5:89766469..89774126-chr5:89823341..89829105,11	K562	blood:
5	chr5:89822684..89827061-chr5:89851623..89857043,7	MCF-7	breast:
6	chr5:89704960..89708059-chr5:89823269..89827144,6	K562	blood:
7	chr5:89768855..89773751-chr5:89822671..89829297,12	K562	blood:
8	chr5:89768691..89773005-chr5:89822332..89827140,9	MCF-7	breast:
9	chr5:89703407..89707223-chr5:89822965..89826833,10	K562	blood:
10	chr5:89822535..89824744-chr5:89842428..89844021,2	K562	blood:
11	chr5:89767818..89772796-chr5:89823286..89827702,11	MCF-7	breast:
12	chr5:89821919..89824561-chr5:89840686..89844146,3	MCF-7	breast:

Variant related genes	Relation type
GPR98	TF binding region
ENSG00000113356	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000176055	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16868767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16868781	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16868783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89773800-89824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:89797600-89824200	Weak transcription	Brain Angular Gyrus	brain
3	chr5:89802600-89824600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:89809000-89824000	Weak transcription	Right Ventricle	heart
5	chr5:89809000-89824400	Weak transcription	Psoas Muscle	Psoas
6	chr5:89809200-89824600	Weak transcription	Spleen	Spleen
7	chr5:89810600-89824400	Weak transcription	Lung	lung
8	chr5:89810800-89824400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:89810800-89824400	Weak transcription	Esophagus	oesophagus
10	chr5:89811000-89824000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:89811000-89824400	Weak transcription	Pancreas	Pancrea
12	chr5:89813400-89824200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:89813400-89824400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:89814800-89824000	Weak transcription	HSMMtube	muscle
15	chr5:89814800-89824200	Weak transcription	Brain Germinal Matrix	brain
16	chr5:89815000-89823800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:89815000-89824400	Weak transcription	Gastric	stomach
18	chr5:89815200-89823800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:89815200-89824400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:89815200-89824400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:89815200-89824400	Weak transcription	Brain Substantia Nigra	brain
22	chr5:89816400-89824200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:89816600-89824000	Weak transcription	Aorta	Aorta
24	chr5:89816600-89824200	Weak transcription	Fetal Brain Male	brain
25	chr5:89816600-89824200	Weak transcription	Ovary	ovary
26	chr5:89817400-89824000	Weak transcription	Fetal Kidney	kidney
27	chr5:89817600-89824200	Weak transcription	Fetal Muscle Leg	muscle
28	chr5:89818000-89824200	Weak transcription	Brain Hippocampus Middle	brain
29	chr5:89818200-89824200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr5:89818200-89824200	Weak transcription	Fetal Stomach	stomach
31	chr5:89818200-89824400	Weak transcription	Left Ventricle	heart
32	chr5:89818600-89824000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr5:89820000-89824000	Weak transcription	Colonic Mucosa	Colon
34	chr5:89820000-89824200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr5:89820400-89824400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:89820800-89824600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:89821000-89824200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr5:89821200-89824000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr5:89821200-89824000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:89821200-89824000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr5:89821200-89824000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:89821200-89824200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr5:89821200-89824200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:89821200-89824200	Weak transcription	Fetal Lung	lung
45	chr5:89821200-89824200	Weak transcription	Placenta	Placenta
46	chr5:89821200-89824200	Weak transcription	HSMM	muscle
47	chr5:89821200-89824400	Weak transcription	Fetal Thymus	thymus
48	chr5:89821600-89824000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:89821800-89824200	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr5:89822000-89824000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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