Variant report

Variant	rs3817092
Chromosome Location	chr15:78764285-78764286
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	chr15:78763504..78765233-chr15:78857709..78859471,2	MCF-7	breast:
2	chr15:78762628..78765009-chr15:78768296..78770207,2	K562	blood:

Variant related genes	Relation type
ENSG00000169684	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10519198	0.88[LWK][hapmap]
rs11634990	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11637193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11639224	0.88[LWK][hapmap]
rs12899131	0.88[LWK][hapmap]
rs16969874	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16969883	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969899	0.91[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969906	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2292116	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2869048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3743079	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57338032	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57839482	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58766815	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61299530	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61388072	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72738715	0.80[EUR][1000 genomes]
rs72738729	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72738743	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72738757	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8036042	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041628	0.88[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv1806890	chr15:78744695-78786064	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3817092	CHRNA5	cis	parietal	SCAN
rs3817092	RASGRF1	cis	parietal	SCAN
rs3817092	IREB2	cis	Whole Blood	GTEx
rs3817092	CHRNA5	cis	cerebellum	SCAN
rs3817092	IREB2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78732200-78799400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:78741200-78781800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:78749000-78764800	Weak transcription	Pancreas	Pancrea
4	chr15:78749000-78767800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:78749800-78764600	Weak transcription	Small Intestine	intestine
6	chr15:78749800-78769600	Weak transcription	Right Ventricle	heart
7	chr15:78750400-78773800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:78751000-78793200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:78752000-78769000	Weak transcription	Psoas Muscle	Psoas
10	chr15:78754000-78789400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr15:78754400-78787600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:78754600-78771200	Strong transcription	HepG2	liver
13	chr15:78754600-78773600	Strong transcription	A549	lung
14	chr15:78754600-78793400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:78754800-78771600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr15:78754800-78793800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr15:78755000-78772800	Strong transcription	Hela-S3	cervix
18	chr15:78755000-78787000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:78755000-78787000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr15:78755000-78793800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:78755000-78794400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr15:78755200-78772200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr15:78755200-78772600	Strong transcription	Primary B cells from cord blood	blood
24	chr15:78755200-78772600	Strong transcription	Osteobl	bone
25	chr15:78755200-78772800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:78755200-78773800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:78755200-78779000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:78755200-78783800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr15:78755200-78787000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:78755200-78792600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr15:78755200-78793400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr15:78755200-78793600	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr15:78755200-78793800	Strong transcription	Fetal Thymus	thymus
34	chr15:78755200-78794000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:78755200-78794600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:78755400-78765800	Strong transcription	Thymus	Thymus
37	chr15:78755400-78766800	Strong transcription	HUVEC	blood vessel
38	chr15:78755400-78767000	Strong transcription	Fetal Lung	lung
39	chr15:78755400-78772800	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr15:78755400-78779000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:78755400-78783200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr15:78755400-78791400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:78755400-78791400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr15:78755400-78791800	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr15:78755400-78792600	Strong transcription	Fetal Muscle Leg	muscle
46	chr15:78755400-78793600	Strong transcription	Liver	Liver
47	chr15:78755600-78772200	Strong transcription	GM12878-XiMat	blood
48	chr15:78755800-78767000	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:78756000-78766200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:78756000-78766800	Strong transcription	NH-A	brain

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