Variant report

Variant	rs16923588
Chromosome Location	chr8:59508076-59508077
allele	A/G
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	PBX3	chr8:59507713-59509008	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr8:59507804-59509028	SK-N-SH	brain:	n/a	n/a
3	MAFK	chr8:59507907-59508200	IMR90	lung:	n/a	chr8:59508028-59508038
4	NFIC	chr8:59507700-59509006	GM12878	blood:	n/a	n/a
5	TCF12	chr8:59507691-59509078	SK-N-SH	brain:	n/a	n/a
6	FOS	chr8:59508003-59508935	HUVEC	blood vessel:	n/a	chr8:59508508-59508518 chr8:59508718-59508728 chr8:59508509-59508517 chr8:59508510-59508517 chr8:59508505-59508516 chr8:59508508-59508518 chr8:59508508-59508518 chr8:59508021-59508033 chr8:59508517-59508526 chr8:59508509-59508517 chr8:59508508-59508518
7	JUND	chr8:59508021-59509007	K562	blood:	n/a	chr8:59508508-59508518 chr8:59508718-59508728 chr8:59508509-59508517 chr8:59508510-59508517 chr8:59508505-59508516 chr8:59508508-59508518 chr8:59508508-59508518 chr8:59508021-59508033 chr8:59508517-59508526 chr8:59508509-59508517 chr8:59508508-59508518
8	BATF	chr8:59507725-59508137	GM12878	blood:	n/a	n/a
9	FOXM1	chr8:59507689-59508217	GM12878	blood:	n/a	n/a
10	STAT3	chr8:59507900-59509004	GM12878	blood:	n/a	n/a
11	MXI1	chr8:59507809-59508085	GM12878	blood:	n/a	n/a
12	EP300	chr8:59507804-59509165	SK-N-SH	brain:	n/a	chr8:59508596-59508610 chr8:59508646-59508660 chr8:59508508-59508517
13	EP300	chr8:59507758-59508138	GM12878	blood:	n/a	n/a
14	RUNX3	chr8:59507645-59508217	GM12878	blood:	n/a	n/a
15	GATA3	chr8:59507804-59509025	SK-N-SH	brain:	n/a	chr8:59508507-59508516
16	SIRT6	chr8:59507988-59508949	K562	blood:	n/a	n/a
17	RCOR1	chr8:59508038-59508978	GM12878	blood:	n/a	n/a
18	NFIC	chr8:59507761-59509058	SK-N-SH	brain:	n/a	n/a
19	EBF1	chr8:59507776-59509075	GM12878	blood:	n/a	n/a
20	EP300	chr8:59507704-59509033	GM12878	blood:	n/a	chr8:59508596-59508610 chr8:59508646-59508660 chr8:59508508-59508517
21	BHLHE40	chr8:59507756-59508087	GM12878	blood:	n/a	n/a
22	GATA3	chr8:59507774-59509123	SK-N-SH	brain:	n/a	chr8:59508507-59508516
23	CHD2	chr8:59507828-59509058	GM12878	blood:	n/a	n/a
24	JUN	chr8:59507122-59509264	K562	blood:	n/a	chr8:59508508-59508518 chr8:59508718-59508728 chr8:59508509-59508517 chr8:59508510-59508517 chr8:59508505-59508516 chr8:59508508-59508518 chr8:59508508-59508518 chr8:59508021-59508033 chr8:59508517-59508526 chr8:59508509-59508517 chr8:59508508-59508518
25	FOS	chr8:59507873-59508925	MCF10A-Er-Src	breast:	n/a	chr8:59508508-59508518 chr8:59508718-59508728 chr8:59508509-59508517 chr8:59508510-59508517 chr8:59508505-59508516 chr8:59508508-59508518 chr8:59508508-59508518 chr8:59508021-59508033 chr8:59508517-59508526 chr8:59508509-59508517 chr8:59508508-59508518
26	FOS	chr8:59508037-59508910	MCF10A-Er-Src	breast:	n/a	chr8:59508508-59508518 chr8:59508718-59508728 chr8:59508509-59508517 chr8:59508510-59508517 chr8:59508505-59508516 chr8:59508508-59508518 chr8:59508508-59508518 chr8:59508517-59508526 chr8:59508509-59508517 chr8:59508508-59508518
27	JUND	chr8:59507741-59509270	SK-N-SH	brain:	n/a	chr8:59508508-59508518 chr8:59508718-59508728 chr8:59508509-59508517 chr8:59508510-59508517 chr8:59508505-59508516 chr8:59508508-59508518 chr8:59508508-59508518 chr8:59508021-59508033 chr8:59508517-59508526 chr8:59508509-59508517 chr8:59508508-59508518

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:59507125..59509829-chr8:59569234..59572145,2	MCF-7	breast:

Variant related genes	Relation type
NSMAF	TF binding region
ENSG00000035681	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10085973	0.88[EUR][1000 genomes]
rs10090425	0.87[EUR][1000 genomes]
rs10094910	0.89[EUR][1000 genomes]
rs10099153	0.82[EUR][1000 genomes]
rs10099240	0.88[EUR][1000 genomes]
rs10099912	0.82[EUR][1000 genomes]
rs10104292	0.96[EUR][1000 genomes]
rs10107530	0.88[EUR][1000 genomes]
rs10111052	0.89[EUR][1000 genomes]
rs10111180	0.82[EUR][1000 genomes]
rs10504256	0.96[EUR][1000 genomes]
rs1050488	0.88[EUR][1000 genomes]
rs1050504	0.81[EUR][1000 genomes]
rs11774558	0.89[EUR][1000 genomes]
rs11782455	0.88[EUR][1000 genomes]
rs11783174	0.81[EUR][1000 genomes]
rs11785141	0.89[EUR][1000 genomes]
rs12335008	0.81[EUR][1000 genomes]
rs12674724	0.80[EUR][1000 genomes]
rs12676593	0.82[EUR][1000 genomes]
rs12677290	0.97[EUR][1000 genomes]
rs12679938	0.82[EUR][1000 genomes]
rs16923594	0.83[EUR][1000 genomes]
rs1976162	0.87[EUR][1000 genomes]
rs2279460	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279462	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28656336	0.80[EUR][1000 genomes]
rs28711402	0.81[EUR][1000 genomes]
rs3739327	0.90[EUR][1000 genomes]
rs3816846	0.89[EUR][1000 genomes]
rs4282557	0.88[EUR][1000 genomes]
rs4400366	0.96[EUR][1000 genomes]
rs4400367	0.88[EUR][1000 genomes]
rs4579515	0.96[EUR][1000 genomes]
rs56249776	0.89[EUR][1000 genomes]
rs59979442	0.82[EUR][1000 genomes]
rs6471731	0.84[EUR][1000 genomes]
rs6991020	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6995115	0.97[EUR][1000 genomes]
rs7011095	0.80[EUR][1000 genomes]
rs72647435	0.81[EUR][1000 genomes]
rs72647437	0.81[EUR][1000 genomes]
rs72647443	0.95[EUR][1000 genomes]
rs7825996	0.81[EUR][1000 genomes]
rs7826122	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7826603	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7827910	0.88[EUR][1000 genomes]
rs7840932	0.97[EUR][1000 genomes]
rs7843989	0.85[EUR][1000 genomes]
rs7844231	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9297996	0.96[EUR][1000 genomes]
rs9297997	0.87[EUR][1000 genomes]
rs9297998	0.96[EUR][1000 genomes]
rs9297999	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890938	chr8:59355053-59809785	Enhancers Strong transcription 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	21 gene(s)	inside rSNPs	diseases
2	nsv890939	chr8:59471187-59544413	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1031537	chr8:59482949-59536971	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv831325	chr8:59492580-59694443	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:59467400-59559400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:59472800-59515800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:59473200-59508600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr8:59477000-59508200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr8:59477600-59514200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:59477800-59508800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr8:59478000-59508200	Strong transcription	Primary B cells from peripheral blood	blood
8	chr8:59478000-59508600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr8:59478000-59508800	Strong transcription	Fetal Intestine Large	intestine
10	chr8:59480600-59515800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr8:59483200-59508800	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr8:59483800-59528000	Strong transcription	Dnd41	blood
13	chr8:59495200-59512800	Strong transcription	Fetal Muscle Leg	muscle
14	chr8:59498600-59511200	Weak transcription	Right Ventricle	heart
15	chr8:59498600-59511800	Weak transcription	Brain Germinal Matrix	brain
16	chr8:59498600-59548400	Weak transcription	Stomach Mucosa	stomach
17	chr8:59500200-59524600	Weak transcription	HepG2	liver
18	chr8:59500600-59521000	Weak transcription	Fetal Heart	heart
19	chr8:59500600-59528800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr8:59502000-59512800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr8:59503000-59545400	Weak transcription	Esophagus	oesophagus
22	chr8:59504200-59508600	Strong transcription	Fetal Thymus	thymus
23	chr8:59504400-59508400	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr8:59504400-59509200	Strong transcription	Liver	Liver
25	chr8:59504400-59510200	Strong transcription	Primary T cells from cord blood	blood
26	chr8:59505200-59510200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr8:59505200-59513000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr8:59505400-59508400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr8:59505400-59508600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr8:59505400-59513000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr8:59505600-59508200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr8:59505600-59508200	Strong transcription	Psoas Muscle	Psoas
33	chr8:59505600-59508200	Genic enhancers	Osteobl	bone
34	chr8:59505600-59508400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr8:59505600-59511000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr8:59505600-59512800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr8:59505800-59510200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr8:59506000-59508400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr8:59506000-59508600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr8:59506000-59508600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr8:59506000-59508800	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr8:59506000-59509000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr8:59506000-59510800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr8:59506000-59513000	Strong transcription	Fetal Lung	lung
45	chr8:59506000-59516800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr8:59506200-59508400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr8:59506200-59508800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr8:59506200-59508800	Genic enhancers	Fetal Brain Male	brain
49	chr8:59506200-59509200	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
50	chr8:59506200-59510200	Strong transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links