Variant report

Variant	rs4887053
Chromosome Location	chr15:78712699-78712700
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78705837..78708183-chr15:78712525..78714255,2	K562	blood:
2	chr15:78711181..78712900-chr15:78728388..78731318,2	MCF-7	breast:
3	chr15:78711992..78713531-chr15:78829665..78831624,2	K562	blood:

Variant related genes	Relation type
ENSG00000268838	Chromatin interaction
ENSG00000136381	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10851906	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11072763	0.81[EUR][1000 genomes]
rs11072766	0.94[CEU][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12101809	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16969894	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2036529	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2036533	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2036534	0.83[CEU][hapmap]
rs2568483	0.80[ASW][hapmap];0.94[CEU][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2568485	0.93[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2568488	0.94[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2568490	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568493	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568497	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568498	0.89[JPT][hapmap]
rs2568499	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2656055	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2656056	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2656069	0.80[ASW][hapmap];0.94[CEU][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2656070	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2656071	1.00[ASW][hapmap];0.94[CEU][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2656072	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2656073	0.94[CEU][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2656074	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28480606	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28511883	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28602670	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2869032	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2869045	0.80[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915695	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2938671	0.88[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2938674	0.94[CEU][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2958719	0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35031105	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3813570	0.83[CEU][hapmap]
rs4461039	0.83[CEU][hapmap]
rs5019044	0.93[CEU][hapmap];0.86[YRI][hapmap]
rs637137	0.80[CEU][hapmap]
rs684513	0.83[CEU][hapmap]
rs7163730	0.82[CEU][hapmap]
rs7164594	0.83[CEU][hapmap]
rs7174190	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7174348	0.80[EUR][1000 genomes]
rs924840	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs958025	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9672608	0.80[EUR][1000 genomes]
rs9788682	0.88[CEU][hapmap]

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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
3	nsv833063	chr15:78605215-78754945	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1627	chr15:78683761-78728604	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4887053	CHRNA5	cis	parietal	SCAN
rs4887053	PML	cis	parietal	SCAN
rs4887053	IREB2	cis	lesional skin	skin_eQTL
rs4887053	CHRNA5	cis	cerebellum	SCAN
rs4887053	FAH	cis	parietal	SCAN
rs4887053	COX5A	cis	parietal	SCAN
rs4887053	PSMA4	cis	parietal	SCAN
rs4887053	IREB2	Cis_1M	lymphoblastoid	RTeQTL
rs4887053	PSMA4	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78698200-78729800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78700800-78722000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:78709800-78715000	Enhancers	HepG2	liver
4	chr15:78710800-78714200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:78710800-78714600	Weak transcription	Colonic Mucosa	Colon
6	chr15:78710800-78715000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr15:78711200-78713600	Enhancers	Placenta	Placenta
8	chr15:78711600-78715000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:78711800-78714000	Weak transcription	Fetal Intestine Large	intestine
10	chr15:78711800-78714600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr15:78711800-78715000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:78712000-78713000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:78712200-78713600	Weak transcription	Fetal Intestine Small	intestine
14	chr15:78712400-78713400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr15:78712400-78713400	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr15:78712400-78713600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:78712600-78712800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr15:78712600-78713000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr15:78712600-78713800	Enhancers	Fetal Muscle Trunk	muscle
20	chr15:78712600-78714400	Enhancers	Fetal Muscle Leg	muscle
21	chr15:78712600-78718000	Weak transcription	Hela-S3	cervix

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