Variant report

Variant	rs34959140
Chromosome Location	chr15:31725223-31725224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31723431..31726207-chr15:31734992..31737659,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1075232	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12437749	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12437800	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12438318	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12438813	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12439239	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12439853	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16956707	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16956738	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4450360	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56249651	0.88[ASN][1000 genomes]
rs56396205	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57924788	0.90[ASN][1000 genomes]
rs58156651	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs66581165	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs67216354	0.88[ASN][1000 genomes]
rs67634762	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs67699697	0.88[ASN][1000 genomes]
rs72722829	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72722847	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72722861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72724938	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72724958	0.90[ASN][1000 genomes]
rs9672214	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9672538	0.94[AMR][1000 genomes];0.92[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	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv3311082	chr15:31724008-31726085	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3311081	chr15:31724038-31726073	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3311083	chr15:31724038-31726073	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv20404	chr15:31724141-31725901	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs34959140	CHRNA7	cis	lung	GTEx
rs34959140	CTD-3092A11.2	cis	lung	GTEx
rs34959140	CTD-3092A11.2	cis	Whole Blood	GTEx
rs34959140	RP11-932O9.7	cis	Artery Tibial	GTEx
rs34959140	RP11-932O9.9	cis	Esophagus Muscularis	GTEx
rs34959140	CHRNA7	cis	Artery Tibial	GTEx
rs34959140	RP11-932O9.7	cis	lung	GTEx
rs34959140	CHRNA7	cis	Whole Blood	GTEx
rs34959140	CHRNA7	cis	Thyroid	GTEx
rs34959140	CTD-3092A11.2	cis	Artery Tibial	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31712800-31732800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:31720200-31725600	Weak transcription	NHDF-Ad	bronchial
3	chr15:31723800-31726800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr15:31724000-31726400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr15:31724000-31726600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:31724000-31727000	Enhancers	Fetal Thymus	thymus
7	chr15:31724200-31726800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr15:31724400-31725400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr15:31724400-31725400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr15:31724400-31725400	Weak transcription	Lung	lung
11	chr15:31724400-31725600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:31724600-31725600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:31724600-31725800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:31724600-31726600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:31724800-31725800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:31724800-31726800	Enhancers	Primary T cells fromperipheralblood	blood
17	chr15:31725000-31726600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr15:31725000-31726800	Enhancers	NHEK	skin
19	chr15:31725200-31725600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr15:31725200-31725800	Enhancers	HMEC	breast
21	chr15:31725200-31726200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:31725200-31726600	Enhancers	Primary T cells from cord blood	blood
23	chr15:31725200-31726800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:31725200-31726800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:31725200-31728200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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