Variant report

Variant	rs2568498
Chromosome Location	chr15:78721932-78721933
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78720134..78723465-chr15:78728938..78732082,4	MCF-7	breast:
2	chr15:78714083..78716832-chr15:78721303..78723382,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136381	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10519198	1.00[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs11072762	0.89[EUR][1000 genomes]
rs11072765	0.93[EUR][1000 genomes]
rs11072766	0.84[JPT][hapmap];0.81[YRI][hapmap]
rs11639224	1.00[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs12899131	0.96[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs12909921	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12910090	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1847529	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2036529	0.83[ASN][1000 genomes]
rs2036532	0.93[EUR][1000 genomes]
rs2568483	0.81[CHD][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs2568485	0.88[JPT][hapmap]
rs2568488	0.90[JPT][hapmap]
rs2568497	0.82[ASN][1000 genomes]
rs2568499	0.82[ASN][1000 genomes]
rs2568500	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs2656055	0.82[ASN][1000 genomes]
rs2656058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656069	0.81[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap]
rs2656071	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs2656073	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs2869032	0.81[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2869045	0.81[CHD][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap]
rs2938671	0.89[JPT][hapmap]
rs2938674	0.89[JPT][hapmap];0.81[YRI][hapmap]
rs2958719	0.86[JPT][hapmap];0.85[YRI][hapmap]
rs4390557	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4436747	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs4887053	0.89[JPT][hapmap]
rs8041628	1.00[CEU][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes]
rs924840	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs954144	0.92[EUR][1000 genomes]

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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2568498	CHRNA5	cis	Heart Left Ventricle	GTEx
rs2568498	IREB2	cis	multi-tissue	Pritchard
rs2568498	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs2568498	CHRNA5	cis	Muscle Skeletal	GTEx
rs2568498	CHRNA5	cis	multi-tissue	Pritchard
rs2568498	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs2568498	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs2568498	CHRNA5	cis	Nerve Tibial	GTEx
rs2568498	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs2568498	RP11-650L12.2	cis	lung	GTEx
rs2568498	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs2568498	CHRNA5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:9 , 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	chr15:78716400-78726200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:78720800-78722400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr15:78720800-78726400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr15:78720800-78728400	Weak transcription	K562	blood
7	chr15:78721000-78726600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr15:78721400-78722600	Enhancers	HepG2	liver
9	chr15:78721800-78722400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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