Variant report

Variant	rs4651073
Chromosome Location	chr1:180600599-180600600
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	PML	chr1:180600336-180601941	GM12878	blood:	n/a	chr1:180601875-180601883
2	RCOR1	chr1:180600369-180601714	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:180600585-180601664	PFSK-1	brain:	n/a	n/a
4	ELF1	chr1:180600323-180600656	K562	blood:	n/a	chr1:180600477-180600490
5	TBL1XR1	chr1:180600472-180600664	K562	blood:	n/a	n/a
6	MXI1	chr1:180600557-180601987	GM12878	blood:	n/a	chr1:180601114-180601129 chr1:180601112-180601127
7	ZNF384	chr1:180600109-180600969	GM12878	blood:	n/a	n/a
8	MXI1	chr1:180600560-180603551	IMR90	lung:	n/a	chr1:180601114-180601129 chr1:180601112-180601127
9	POLR2A	chr1:180600256-180601905	Raji	blood:	n/a	n/a
10	CHD1	chr1:180600439-180600807	GM12878	blood:	n/a	n/a
11	REST	chr1:180600552-180603720	H1-neurons	neurons:	n/a	chr1:180602973-180602993 chr1:180601797-180601810 chr1:180602973-180602993 chr1:180602973-180602987
12	EBF1	chr1:180600178-180600653	GM12878	blood:	n/a	chr1:180600444-180600454 chr1:180600443-180600456 chr1:180600443-180600454 chr1:180600445-180600454 chr1:180600445-180600454
13	EBF1	chr1:180600206-180600664	GM12878	blood:	n/a	chr1:180600444-180600454 chr1:180600443-180600456 chr1:180600443-180600454 chr1:180600445-180600454 chr1:180600445-180600454
14	MAZ	chr1:180600545-180601876	HepG2	liver:	n/a	chr1:180601114-180601123
15	CTCF	chr1:180600560-180600710	RPTEC	kidney:	n/a	n/a
16	EBF1	chr1:180600187-180601344	GM12878	blood:	n/a	chr1:180600444-180600454 chr1:180600443-180600456 chr1:180600443-180600454 chr1:180600445-180600454 chr1:180600445-180600454
17	HCFC1	chr1:180600560-180601888	K562	blood:	n/a	n/a
18	CHD2	chr1:180600208-180601930	GM12878	blood:	n/a	chr1:180601649-180601656
19	POLR2A	chr1:180600413-180602066	PBDE	blood:	n/a	n/a
20	POLR2A	chr1:180600406-180600605	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:180486117..180489431-chr1:180599413..180603700,5	MCF-7	breast:
2	chr1:180599642..180602569-chr1:180990925..180993189,3	MCF-7	breast:
3	chr1:180599613..180601233-chr1:180805149..180807716,2	K562	blood:
4	chr1:180470531..180473320-chr1:180599332..180602016,2	K562	blood:
5	chr1:180470493..180473506-chr1:180597830..180602116,4	MCF-7	breast:
6	chr1:180598794..180600928-chr1:181056427..181059135,2	K562	blood:

Variant related genes	Relation type
XPR1	TF binding region
ENSG00000135847	Chromatin interaction
ENSG00000143324	Chromatin interaction
ENSG00000162783	Chromatin interaction
ENSG00000135823	Chromatin interaction
ENSG00000206905	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10914096	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12118646	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1339768	1.00[CHB][hapmap]
rs1970404	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2331626	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs3002114	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3002117	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs3002123	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs3753202	0.94[ASN][1000 genomes]
rs3819951	0.92[ASN][1000 genomes]
rs3819953	0.95[ASN][1000 genomes]
rs3843278	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs3845406	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs3856058	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6661105	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs7541650	0.87[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap]
rs9425881	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9970145	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs9970363	0.91[CHB][hapmap]

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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4651073	RABGAP1L	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180581800-180600600	Weak transcription	Fetal Heart	heart
2	chr1:180593200-180601000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:180599000-180600800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:180599200-180600800	Enhancers	Adipose Nuclei	Adipose
5	chr1:180599400-180600600	Enhancers	Left Ventricle	heart
6	chr1:180599400-180600800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:180599400-180600800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:180599400-180600800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:180599400-180601000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:180599400-180601000	Enhancers	Osteobl	bone
11	chr1:180599600-180600600	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr1:180599600-180601000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:180599600-180601200	Weak transcription	Right Atrium	heart
14	chr1:180599600-180601200	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr1:180599800-180600600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:180599800-180600600	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr1:180599800-180601000	Enhancers	Primary B cells from peripheral blood	blood
18	chr1:180600000-180600600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr1:180600000-180600600	Enhancers	GM12878-XiMat	blood
20	chr1:180600000-180600800	Enhancers	Right Ventricle	heart
21	chr1:180600000-180601000	Enhancers	Fetal Intestine Large	intestine
22	chr1:180600000-180601200	Enhancers	Primary B cells from cord blood	blood
23	chr1:180600200-180600600	Active TSS	Brain Substantia Nigra	brain
24	chr1:180600200-180600600	Enhancers	Fetal Thymus	thymus
25	chr1:180600200-180600800	Enhancers	Fetal Kidney	kidney
26	chr1:180600200-180600800	Enhancers	Psoas Muscle	Psoas
27	chr1:180600200-180600800	Flanking Active TSS	HepG2	liver
28	chr1:180600200-180600800	Enhancers	K562	blood
29	chr1:180600200-180601000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:180600200-180601000	Enhancers	Stomach Mucosa	stomach
31	chr1:180600200-180601200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr1:180600200-180601200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:180600400-180600600	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr1:180600400-180600600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr1:180600400-180600600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:180600400-180600600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:180600400-180600600	Enhancers	Brain Hippocampus Middle	brain
38	chr1:180600400-180600600	Enhancers	Colonic Mucosa	Colon
39	chr1:180600400-180600600	Enhancers	Colon Smooth Muscle	Colon
40	chr1:180600400-180600600	Enhancers	Esophagus	oesophagus
41	chr1:180600400-180600600	Enhancers	Lung	lung
42	chr1:180600400-180600600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr1:180600400-180600600	Enhancers	Spleen	Spleen
44	chr1:180600400-180600600	Enhancers	A549	lung
45	chr1:180600400-180600800	Enhancers	H1 Cell Line	embryonic stem cell
46	chr1:180600400-180600800	Enhancers	Primary hematopoietic stem cells	blood
47	chr1:180600400-180600800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr1:180600400-180600800	Enhancers	Brain Anterior Caudate	brain
49	chr1:180600400-180600800	Enhancers	Brain Cingulate Gyrus	brain
50	chr1:180600400-180600800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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