Variant report

Variant	rs11638674
Chromosome Location	chr15:77891940-77891941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77884388..77887095-chr15:77890695..77892603,2	K562	blood:
2	chr15:77890205..77893278-chr15:77923097..77926362,3	K562	blood:
3	chr15:77890507..77893828-chr15:77894009..77899298,4	MCF-7	breast:
4	chr15:77891327..77896574-chr15:77898422..77902980,9	K562	blood:
5	chr15:77866782..77869407-chr15:77890484..77892735,2	MCF-7	breast:
6	chr15:77891099..77895017-chr15:77905947..77909078,4	K562	blood:
7	chr15:77884788..77887533-chr15:77890079..77892791,3	K562	blood:

Variant related genes	Relation type
ENSG00000169783	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1104815	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs11630235	0.94[CEU][hapmap]
rs11631894	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11633811	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs11635834	0.80[EUR][1000 genomes]
rs11636780	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11638351	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16968998	0.94[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16968999	0.94[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2003883	0.80[EUR][1000 genomes]
rs28368579	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28477219	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28706124	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3144	0.82[GIH][hapmap];0.81[TSI][hapmap]
rs4286073	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886517	0.81[EUR][1000 genomes]
rs4886882	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886884	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886885	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886886	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886887	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4886888	0.94[CEU][hapmap];0.97[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7171141	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8039399	0.89[CEU][hapmap];0.89[AMR][1000 genomes]
rs868298	0.82[EUR][1000 genomes]
rs884527	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9806139	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv904415	chr15:77845959-77943935	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv904416	chr15:77845959-77967416	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv904417	chr15:77851535-77935992	Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904418	chr15:77851535-77963887	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1036749	chr15:77884026-77912408	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11638674	STRA6	cis	cerebellum	SCAN
rs11638674	CHRNA5	cis	cerebellum	SCAN
rs11638674	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL
rs11638674	HMG20A	cis	parietal	SCAN
rs11638674	CHRNA5	cis	parietal	SCAN
rs11638674	CYP1A2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77875600-77892000	Weak transcription	Right Atrium	heart
2	chr15:77883800-77896000	Weak transcription	Brain Hippocampus Middle	brain
3	chr15:77888200-77892000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr15:77889400-77892000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:77889400-77892200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:77889400-77896000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:77889800-77892600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:77889800-77896400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:77890200-77892000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr15:77890200-77892800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr15:77890600-77892200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:77890800-77892000	Weak transcription	Right Ventricle	heart
13	chr15:77890800-77892200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:77891000-77896600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:77891000-77898800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:77891200-77893000	Enhancers	Fetal Stomach	stomach
17	chr15:77891200-77893400	Enhancers	Fetal Heart	heart
18	chr15:77891600-77892600	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr15:77891800-77892000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:77891800-77892400	Enhancers	Lung	lung
21	chr15:77891800-77892800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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