Variant report

Variant	rs576888
Chromosome Location	chr1:84853611-84853612
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:93)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:93 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:84853560-84853710	BE2_C	brain:	n/a	n/a
2	CTCF	chr1:84853500-84853650	HPF	lung:	n/a	n/a
3	CTCF	chr1:84853540-84853690	K562	blood:	n/a	n/a
4	CTCF	chr1:84853520-84853670	RPTEC	kidney:	n/a	n/a
5	RAD21	chr1:84853410-84853771	ECC-1	luminal epithelium:	n/a	n/a
6	CTCF	chr1:84853469-84853767	Gliobla	brain:	n/a	n/a
7	RAD21	chr1:84853459-84853745	IMR90	lung:	n/a	n/a
8	CTCF	chr1:84853540-84853690	HCPEpiC	choroid plexus:	n/a	n/a
9	CTCF	chr1:84853500-84853650	RPTEC	kidney:	n/a	n/a
10	CTCF	chr1:84853500-84853650	GM12865	blood:	n/a	n/a
11	CTCF	chr1:84853560-84853710	NHDF-neo	bronchial:	n/a	n/a
12	CTCF	chr1:84853406-84853750	K562	blood:	n/a	n/a
13	CTCF	chr1:84853500-84853650	NHLF	lung:	n/a	n/a
14	RAD21	chr1:84853330-84853818	H1-hESC	embryonic stem cell:	n/a	n/a
15	GATA2	chr1:84853360-84853724	HUVEC	blood vessel:	n/a	n/a
16	CTCF	chr1:84853497-84853751	ProgFib	skin:	n/a	n/a
17	CTCF	chr1:84853580-84853730	HCPEpiC	choroid plexus:	n/a	n/a
18	CTCF	chr1:84853580-84853730	HVMF	connective:	n/a	n/a
19	CTCF	chr1:84853520-84853670	HPAF	blood vessel:	n/a	n/a
20	RAD21	chr1:84853422-84853775	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr1:84853540-84853690	HAc	cerebellar:	n/a	n/a
22	CTCF	chr1:84853540-84853690	HCFaa	heart:	n/a	n/a
23	CTCF	chr1:84853447-84853773	H1-hESC	embryonic stem cell:	n/a	n/a
24	RAD21	chr1:84853514-84853693	K562	blood:	n/a	n/a
25	CTCF	chr1:84853540-84853690	GM12871	blood:	n/a	n/a
26	CTCF	chr1:84853552-84853690	Fibrobl	skin:	n/a	n/a
27	RAD21	chr1:84853279-84853979	HCT-116	colon:	n/a	n/a
28	CTCF	chr1:84853424-84853853	K562	blood:	n/a	n/a
29	CTCF	chr1:84853520-84853670	HA-sp	spinal cord:	n/a	n/a
30	CTCF	chr1:84853540-84853690	HBMEC	blood vessel:	n/a	n/a
31	CTCF	chr1:84853520-84853670	HPF	lung:	n/a	n/a
32	CTCF	chr1:84853500-84853650	MCF-7	breast:	n/a	n/a
33	CTCF	chr1:84853500-84853650	HFF-Myc	foreskin:	n/a	n/a
34	CTCF	chr1:84853324-84853785	K562	blood:	n/a	n/a
35	CTCF	chr1:84853540-84853690	AG09319	gingival:	n/a	n/a
36	CTCF	chr1:84853537-84853696	HepG2	liver:	n/a	n/a
37	SMC3	chr1:84853432-84853781	K562	blood:	n/a	n/a
38	ZNF143	chr1:84853472-84853742	K562	blood:	n/a	n/a
39	RAD21	chr1:84853379-84853808	SK-N-SH_RA	brain:	n/a	n/a
40	CTCF	chr1:84853560-84853710	HCT-116	colon:	n/a	n/a
41	CBX3	chr1:84852779-84853919	HCT-116	colon:	n/a	n/a
42	RAD21	chr1:84853466-84853802	MCF-7	breast:	n/a	n/a
43	CTCF	chr1:84853540-84853690	GM12874	blood:	n/a	n/a
44	CTCF	chr1:84853486-84853714	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr1:84853515-84853745	K562	blood:	n/a	n/a
46	RCOR1	chr1:84853426-84853776	K562	blood:	n/a	n/a
47	CTCF	chr1:84853500-84853650	HRE	kidney:	n/a	n/a
48	CTCF	chr1:84853520-84853670	NB4	blood:	n/a	n/a
49	CTCF	chr1:84853576-84853660	Medullo	brain:	n/a	n/a
50	CTCF	chr1:84853500-84853650	HAc	cerebellar:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84853389..84854043-chr1:85237940..85238620,2	K562	blood:

No data

Variant related genes	Relation type
UOX	TF binding region

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12039378	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12042948	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12044734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568281	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131659	0.84[ASW][hapmap]
rs2275571	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs315512	0.90[ASN][1000 genomes]
rs477253	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507863	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508767	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548310	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580171	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585958	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636484	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649845	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666062	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696653	0.91[EUR][1000 genomes]
rs7554646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830426	chr1:84704924-84856229	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs576888	LPAR3	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84845600-84857200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:84845800-84854800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:84846400-84856000	Weak transcription	NHLF	lung
4	chr1:84852000-84857200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:84852200-84853800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:84853200-84855800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:84853400-84854800	Enhancers	GM12878-XiMat	blood
8	chr1:84853400-84855800	Weak transcription	HMEC	breast
9	chr1:84853600-84855800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:84853600-84855800	Weak transcription	NHEK	skin
11	chr1:84853600-84857800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:84853600-84858800	Weak transcription	HUVEC	blood vessel

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