Variant report

Variant	rs2279462
Chromosome Location	chr8:59507950-59507951
allele	G/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	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	BATF	chr8:59507725-59508137	GM12878	blood:	n/a	n/a
7	FOXM1	chr8:59507689-59508217	GM12878	blood:	n/a	n/a
8	STAT3	chr8:59507900-59509004	GM12878	blood:	n/a	n/a
9	WRNIP1	chr8:59507690-59508000	GM12878	blood:	n/a	n/a
10	MXI1	chr8:59507809-59508085	GM12878	blood:	n/a	n/a
11	EP300	chr8:59507804-59509165	SK-N-SH	brain:	n/a	chr8:59508596-59508610 chr8:59508646-59508660 chr8:59508508-59508517
12	EP300	chr8:59507758-59508138	GM12878	blood:	n/a	n/a
13	RUNX3	chr8:59507645-59508217	GM12878	blood:	n/a	n/a
14	STAT1	chr8:59507817-59507985	GM12878	blood:	n/a	n/a
15	CTCF	chr8:59507855-59508041	GM12878	blood:	n/a	n/a
16	GATA3	chr8:59507804-59509025	SK-N-SH	brain:	n/a	chr8:59508507-59508516
17	RUNX3	chr8:59507721-59508060	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	TBP	chr8:59507889-59508066	GM12878	blood:	n/a	n/a
27	ZNF143	chr8:59507709-59508053	GM12878	blood:	n/a	n/a
28	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: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10085973	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs10090425	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs10090964	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs10091952	0.82[EUR][1000 genomes]
rs10092359	0.85[EUR][1000 genomes]
rs10094910	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10099153	0.87[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs10099240	0.82[EUR][1000 genomes]
rs10099912	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs10102709	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs10104292	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10107530	0.95[EUR][1000 genomes]
rs10110111	0.81[EUR][1000 genomes]
rs10111052	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10111180	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10111506	0.82[EUR][1000 genomes]
rs10113323	0.80[CEU][hapmap]
rs10113750	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs10113830	0.80[EUR][1000 genomes]
rs10504256	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1050488	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs1050504	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs11774558	0.97[EUR][1000 genomes]
rs11776003	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs11782455	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11783174	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs11785141	0.97[EUR][1000 genomes]
rs12335008	0.88[EUR][1000 genomes]
rs12674568	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs12674724	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12676593	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs12677290	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12679938	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs12680104	0.81[EUR][1000 genomes]
rs12680996	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs1352496	0.80[EUR][1000 genomes]
rs16923562	0.81[EUR][1000 genomes]
rs16923564	0.82[EUR][1000 genomes]
rs16923588	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16923594	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17206746	0.82[EUR][1000 genomes]
rs17263989	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs17272151	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs1976162	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1991359	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2130072	0.86[EUR][1000 genomes]
rs2255834	0.90[JPT][hapmap]
rs2279460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634527	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2634530	0.91[JPT][hapmap]
rs2634531	0.86[JPT][hapmap]
rs2680897	0.91[JPT][hapmap]
rs2680899	0.90[JPT][hapmap]
rs28429491	0.82[EUR][1000 genomes]
rs28650441	0.82[EUR][1000 genomes]
rs28656336	0.87[EUR][1000 genomes]
rs28711402	0.88[EUR][1000 genomes]
rs3739327	0.83[EUR][1000 genomes]
rs3808609	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs3816846	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4282557	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs4400366	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4400367	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs4579515	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4737504	0.81[JPT][hapmap]
rs55774738	0.82[EUR][1000 genomes]
rs56249776	0.97[EUR][1000 genomes]
rs59979442	0.89[EUR][1000 genomes]
rs6471729	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs6981601	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs6986129	0.82[EUR][1000 genomes]
rs6987187	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6991020	0.80[EUR][1000 genomes]
rs6995115	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7009248	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs7009374	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs7011095	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs7014398	0.81[EUR][1000 genomes]
rs72647434	0.86[EUR][1000 genomes]
rs72647435	0.88[EUR][1000 genomes]
rs72647437	0.88[EUR][1000 genomes]
rs72647443	0.89[EUR][1000 genomes]
rs7817515	0.81[EUR][1000 genomes]
rs7820921	0.80[JPT][hapmap]
rs7825996	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs7826122	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7826603	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7827910	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs7840932	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7844231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9297995	0.81[EUR][1000 genomes]
rs9297996	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9297997	0.87[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs9297998	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9297999	0.87[CEU][hapmap];0.87[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	chr8:59479600-59508000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr8:59480600-59515800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr8:59483200-59508800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr8:59483800-59528000	Strong transcription	Dnd41	blood
14	chr8:59495200-59512800	Strong transcription	Fetal Muscle Leg	muscle
15	chr8:59498600-59511200	Weak transcription	Right Ventricle	heart
16	chr8:59498600-59511800	Weak transcription	Brain Germinal Matrix	brain
17	chr8:59498600-59548400	Weak transcription	Stomach Mucosa	stomach
18	chr8:59500200-59524600	Weak transcription	HepG2	liver
19	chr8:59500600-59521000	Weak transcription	Fetal Heart	heart
20	chr8:59500600-59528800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr8:59502000-59508000	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr8:59502000-59512800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr8:59503000-59508000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr8:59503000-59545400	Weak transcription	Esophagus	oesophagus
25	chr8:59504200-59508600	Strong transcription	Fetal Thymus	thymus
26	chr8:59504400-59508400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr8:59504400-59509200	Strong transcription	Liver	Liver
28	chr8:59504400-59510200	Strong transcription	Primary T cells from cord blood	blood
29	chr8:59505200-59508000	Strong transcription	Fetal Intestine Small	intestine
30	chr8:59505200-59510200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr8:59505200-59513000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr8:59505400-59508400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr8:59505400-59508600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr8:59505400-59513000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr8:59505600-59508000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr8:59505600-59508200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr8:59505600-59508200	Strong transcription	Psoas Muscle	Psoas
38	chr8:59505600-59508200	Genic enhancers	Osteobl	bone
39	chr8:59505600-59508400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr8:59505600-59511000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr8:59505600-59512800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr8:59505800-59510200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr8:59506000-59508000	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr8:59506000-59508400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr8:59506000-59508600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr8:59506000-59508600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr8:59506000-59508800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr8:59506000-59509000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr8:59506000-59510800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr8:59506000-59513000	Strong transcription	Fetal Lung	lung

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