Variant report

Variant	rs2869045
Chromosome Location	chr15:78718899-78718900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78718625..78720309-chr15:78729352..78732262,2	K562	blood:

Variant related genes	Relation type
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	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072763	0.85[EUR][1000 genomes]
rs11072766	0.94[CEU][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12101809	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16969894	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2036529	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2036533	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2036534	0.83[CEU][hapmap]
rs2568483	1.00[ASW][hapmap];0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2568485	0.93[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568488	0.94[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568490	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2568493	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2568497	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568498	0.81[CHD][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap]
rs2568499	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656055	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656056	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2656069	1.00[ASW][hapmap];0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2656070	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2656071	0.80[ASW][hapmap];0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2656072	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2656073	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2656074	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28480606	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28511883	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28602670	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2869032	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915695	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2938671	0.88[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2938674	0.94[CEU][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2958719	0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35031105	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3813570	0.83[CEU][hapmap]
rs4461039	0.83[CEU][hapmap]
rs4887053	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]
rs5019044	0.93[CEU][hapmap]
rs637137	0.80[CEU][hapmap]
rs684513	0.83[CEU][hapmap]
rs7163730	0.82[CEU][hapmap]
rs7164594	0.83[CEU][hapmap]
rs7174190	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7174348	0.84[EUR][1000 genomes]
rs924840	0.80[ASW][hapmap];0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs958025	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9672608	0.82[AMR][1000 genomes];0.84[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
rs2869045	IREB2	cis	lesional skin	skin_eQTL
rs2869045	FAH	cis	parietal	SCAN
rs2869045	CHRNA5	cis	parietal	SCAN
rs2869045	IREB2	Cis_1M	lymphoblastoid	RTeQTL
rs2869045	PSMA4	cis	parietal	SCAN
rs2869045	PSMA4	cis	cerebellum	SCAN
rs2869045	CHRNA5	cis	cerebellum	SCAN
rs2869045	PML	cis	parietal	SCAN
rs2869045	COX5A	cis	parietal	SCAN

Chromatin state (count:15 , 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	chr15:78715000-78720800	Enhancers	Primary hematopoietic stem cells	blood
4	chr15:78715000-78721000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:78716400-78726200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr15:78717000-78719200	Enhancers	Dnd41	blood
7	chr15:78717200-78719000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:78717200-78719800	Weak transcription	K562	blood
9	chr15:78717400-78719200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr15:78717600-78719000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr15:78717600-78719000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr15:78718600-78720600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr15:78718800-78719600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr15:78718800-78719800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr15:78718800-78721000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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