Variant report

Variant	rs4526543
Chromosome Location	chrX:153878001-153878002
allele	C/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	ESR1	chrX:153877917-153878243	T-47D	breast:	n/a	chrX:153878100-153878117 chrX:153878065-153878082 chrX:153878099-153878116 chrX:153878065-153878080 chrX:153878064-153878081 chrX:153878100-153878115
2	ESR1	chrX:153877921-153878694	T-47D	breast:	n/a	chrX:153878100-153878117 chrX:153878065-153878082 chrX:153878099-153878116 chrX:153878065-153878080 chrX:153878426-153878443 chrX:153878064-153878081 chrX:153878100-153878115
3	TCF12	chrX:153877679-153878350	MCF-7	breast:	n/a	chrX:153877759-153877769 chrX:153877874-153877884
4	TCF12	chrX:153877789-153878300	MCF-7	breast:	n/a	chrX:153877874-153877884
5	ESR1	chrX:153877844-153878304	T-47D	breast:	n/a	chrX:153878100-153878117 chrX:153878065-153878082 chrX:153878099-153878116 chrX:153878065-153878080 chrX:153878064-153878081 chrX:153878100-153878115
6	ESR1	chrX:153877795-153878798	ECC-1	luminal epithelium:	n/a	chrX:153878100-153878117 chrX:153878065-153878082 chrX:153878099-153878116 chrX:153878065-153878080 chrX:153878426-153878443 chrX:153878064-153878081 chrX:153878100-153878115
7	NR2F2	chrX:153877752-153878345	MCF-7	breast:	n/a	n/a
8	ESR1	chrX:153877879-153878218	ECC-1	luminal epithelium:	n/a	chrX:153878100-153878117 chrX:153878065-153878082 chrX:153878099-153878116 chrX:153878065-153878080 chrX:153878064-153878081 chrX:153878100-153878115
9	EP300	chrX:153877849-153878359	MCF-7	breast:	n/a	n/a
10	ESR1	chrX:153877862-153878181	ECC-1	luminal epithelium:	n/a	chrX:153878100-153878117 chrX:153878065-153878082 chrX:153878099-153878116 chrX:153878065-153878080 chrX:153878064-153878081 chrX:153878100-153878115
11	ESR1	chrX:153877882-153878648	ECC-1	luminal epithelium:	n/a	chrX:153878100-153878117 chrX:153878065-153878082 chrX:153878099-153878116 chrX:153878065-153878080 chrX:153878426-153878443 chrX:153878064-153878081 chrX:153878100-153878115
12	SIN3AK20	chrX:153877714-153878413	MCF-7	breast:	n/a	n/a
13	ESR1	chrX:153877835-153878795	ECC-1	luminal epithelium:	n/a	chrX:153878100-153878117 chrX:153878065-153878082 chrX:153878099-153878116 chrX:153878065-153878080 chrX:153878426-153878443 chrX:153878064-153878081 chrX:153878100-153878115
14	MAX	chrX:153877869-153878286	MCF-7	breast:	n/a	chrX:153878128-153878144 chrX:153878194-153878201
15	ESR1	chrX:153877909-153878488	T-47D	breast:	n/a	chrX:153878100-153878117 chrX:153878065-153878082 chrX:153878099-153878116 chrX:153878065-153878080 chrX:153878426-153878443 chrX:153878064-153878081 chrX:153878100-153878115
16	GATA3	chrX:153877827-153878302	MCF-7	breast:	n/a	n/a
17	ESR1	chrX:153877822-153878293	ECC-1	luminal epithelium:	n/a	chrX:153878100-153878117 chrX:153878065-153878082 chrX:153878099-153878116 chrX:153878065-153878080 chrX:153878064-153878081 chrX:153878100-153878115
18	HA-E2F1	chrX:153877825-153878431	MCF-7	breast:	n/a	n/a
19	ESR1	chrX:153877885-153878195	T-47D	breast:	n/a	chrX:153878100-153878117 chrX:153878065-153878082 chrX:153878099-153878116 chrX:153878065-153878080 chrX:153878064-153878081 chrX:153878100-153878115

No.	Distal block	Cell Line	Cell type
1	chrX:153718876..153719771-chrX:153877675..153878348,2	MCF-7	breast:
2	chrX:153647888..153648853-chrX:153877953..153878815,7	MCF-7	breast:
3	chrX:153769248..153770465-chrX:153877772..153878953,6	MCF-7	breast:
4	chrX:153770673..153771411-chrX:153877763..153878515,2	MCF-7	breast:
5	chrX:153647888..153648798-chrX:153877953..153878815,5	MCF-7	breast:
6	chrX:153877950..153878544-chrX:154216332..154217020,2	MCF-7	breast:
7	chrX:153877989..153878508-chrX:153926907..153927860,2	MCF-7	breast:
8	chr8:102132680..102133483-chrX:153877983..153878973,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226141	TF binding region
IKBKGP1	TF binding region
ENSG00000102125	Chromatin interaction
ENSG00000073009	Chromatin interaction
ENSG00000126903	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10127172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs1848763	0.89[CHB][hapmap]
rs2664170	0.89[CHB][hapmap]
rs2728526	0.89[CHB][hapmap]
rs2728530	0.85[ASW][hapmap];1.00[CHB][hapmap];0.86[MKK][hapmap]
rs2728725	0.89[CHB][hapmap]
rs2728729	0.80[JPT][hapmap]
rs4326559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs4431759	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap]
rs4898348	0.94[MEX][hapmap]
rs5945108	0.89[MEX][hapmap]
rs5945222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs5945223	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs5945224	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs5987005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs5987011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap]
rs5987015	0.89[CHB][hapmap]
rs5987016	0.89[CHB][hapmap]
rs6643615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6643620	1.00[LWK][hapmap];0.86[YRI][hapmap]
rs884840	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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	esv3648994	chrX:153829693-153919915	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv518228	chrX:153829693-153919915	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3347979	chrX:153836429-153878781	Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4526543	PLXNA3	cis	multi-tissue	Pritchard

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153877200-153878600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chrX:153877400-153878600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chrX:153877600-153878400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chrX:153877600-153878400	Bivalent Enhancer	Fetal Muscle Leg	muscle
5	chrX:153877600-153878600	Enhancers	Ovary	ovary
6	chrX:153877600-153878800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chrX:153877800-153878600	Bivalent Enhancer	Placenta	Placenta
8	chrX:153878000-153878400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
9	chrX:153878000-153878600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chrX:153878000-153878600	Enhancers	HUVEC	blood vessel
11	chrX:153878000-153879600	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links