Variant report

Variant	rs6425513
Chromosome Location	chr1:179006462-179006463
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	FOS	chr1:179006263-179006599	MCF10A-Er-Src	breast:	n/a	chr1:179006431-179006442
2	BCLAF1	chr1:179006133-179006576	GM12878	blood:	n/a	chr1:179006391-179006400
3	MTA3	chr1:179006001-179006642	GM12878	blood:	n/a	n/a
4	RCOR1	chr1:179006168-179006547	K562	blood:	n/a	n/a
5	EP300	chr1:179006039-179006570	GM12878	blood:	n/a	chr1:179006062-179006076 chr1:179006069-179006078
6	ZNF384	chr1:179006215-179006730	GM12878	blood:	n/a	n/a
7	ZNF384	chr1:179006323-179006726	K562	blood:	n/a	n/a
8	EBF1	chr1:179006235-179006562	GM12878	blood:	n/a	n/a
9	IKZF1	chr1:179006130-179006472	GM12878	blood:	n/a	n/a
10	JUN	chr1:179006257-179006472	K562	blood:	n/a	n/a
11	NFIC	chr1:179006147-179006675	GM12878	blood:	n/a	n/a
12	RUNX3	chr1:179006136-179006643	GM12878	blood:	n/a	n/a
13	FOS	chr1:179006214-179006604	HUVEC	blood vessel:	n/a	chr1:179006431-179006442
14	CUX1	chr1:179006393-179006594	GM12878	blood:	n/a	n/a
15	PBX3	chr1:179006098-179006689	SK-N-SH	brain:	n/a	n/a
16	BATF	chr1:179006241-179006574	GM12878	blood:	n/a	chr1:179006433-179006444
17	PBX3	chr1:179006275-179006499	GM12878	blood:	n/a	n/a
18	ATF2	chr1:179006167-179006659	GM12878	blood:	n/a	n/a
19	PBX3	chr1:179006199-179006612	SK-N-SH	brain:	n/a	n/a
20	RUNX3	chr1:179006125-179006640	GM12878	blood:	n/a	n/a
21	BATF	chr1:179006201-179006570	GM12878	blood:	n/a	chr1:179006433-179006444
22	FOS	chr1:179006294-179006567	MCF10A-Er-Src	breast:	n/a	chr1:179006431-179006442
23	JUND	chr1:179006215-179006547	K562	blood:	n/a	n/a
24	EP300	chr1:179006186-179006571	GM12878	blood:	n/a	n/a
25	STAT3	chr1:179006292-179006462	MCF10A-Er-Src	breast:	n/a	chr1:179006391-179006402
26	FOS	chr1:179006333-179006533	MCF10A-Er-Src	breast:	n/a	chr1:179006431-179006442
27	BCL11A	chr1:179006275-179006517	GM12878	blood:	n/a	chr1:179006391-179006400

No.	Distal block	Cell Line	Cell type
1	chr1:179006443..179009675-chr1:179013601..179018312,6	K562	blood:
2	chr1:179006443..179009828-chr1:179013760..179016314,4	K562	blood:
3	chr1:179006020..179008599-chr1:179014929..179016616,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232750	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10798649	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10798650	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10798651	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10913682	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1220	1.00[ASW][hapmap];0.80[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs12743735	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2025584	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3753533	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3766626	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3766628	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3820163	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4297249	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4652351	0.90[AMR][1000 genomes]
rs61823786	0.87[EUR][1000 genomes]
rs7515519	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7526438	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7549040	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs912758	0.91[CEU][hapmap];0.85[CHB][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9283394	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9725887	0.87[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs9727621	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9727648	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6425513	RALGPS2	cis	parietal	SCAN
rs6425513	FAM20B	cis	parietal	SCAN
rs6425513	FAM20B	cis	cerebellum	SCAN
rs6425513	TOR3A	cis	Artery Tibial	GTEx
rs6425513	FAM20B	cis	lymphoblastoid	seeQTL
rs6425513	ABL2	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:178996200-179009200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:178996400-179011200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:178998200-179008600	Enhancers	Colon Smooth Muscle	Colon
4	chr1:178998400-179027400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:178998600-179007600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:178998600-179008000	Weak transcription	Placenta	Placenta
7	chr1:178999000-179009600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:179001200-179008600	Enhancers	Primary B cells from peripheral blood	blood
9	chr1:179001200-179009600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:179001400-179007600	Weak transcription	Fetal Brain Female	brain
11	chr1:179001600-179017000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:179001800-179008600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr1:179001800-179016200	Weak transcription	Aorta	Aorta
14	chr1:179002000-179019200	Weak transcription	Adipose Nuclei	Adipose
15	chr1:179002200-179007600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:179002800-179008600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:179003200-179008600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:179003400-179007200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:179003600-179007200	Weak transcription	Ovary	ovary
20	chr1:179003600-179009200	Weak transcription	Right Ventricle	heart
21	chr1:179003800-179011200	Weak transcription	Thymus	Thymus
22	chr1:179003800-179025800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:179004000-179007600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:179004000-179008000	Enhancers	NHDF-Ad	bronchial
25	chr1:179004000-179011000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:179004200-179007600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:179004200-179007600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:179004200-179007800	Weak transcription	Brain Anterior Caudate	brain
29	chr1:179004200-179009200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:179004200-179010800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:179004200-179024200	Weak transcription	Liver	Liver
32	chr1:179004400-179007200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:179004400-179007200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:179004400-179007400	Weak transcription	HepG2	liver
35	chr1:179004400-179007600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:179004400-179007600	Weak transcription	Fetal Heart	heart
37	chr1:179004400-179008200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:179004400-179012800	Weak transcription	Fetal Lung	lung
39	chr1:179004400-179013000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:179004400-179019200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:179004400-179024200	Weak transcription	Fetal Kidney	kidney
42	chr1:179004600-179007200	Weak transcription	Fetal Thymus	thymus
43	chr1:179004600-179007600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:179004600-179007600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:179004600-179007800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:179004600-179007800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:179004600-179007800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:179004800-179007200	Weak transcription	Right Atrium	heart
49	chr1:179004800-179007600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:179004800-179011200	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links