Variant report

Variant	rs16969899
Chromosome Location	chr15:78782326-78782327
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:78782132-78782690	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:78781862-78782518	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:78781665-78783737	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78780872..78783666-chr15:78797179..78800862,3	K562	blood:

Variant related genes	Relation type
IREB2	TF binding region
ENSG00000188266	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10519198	0.85[LWK][hapmap]
rs11634990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11637193	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11639224	0.85[LWK][hapmap]
rs12899131	0.85[LWK][hapmap]
rs16969874	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16969883	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2292116	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2869048	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3743079	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3817092	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]
rs57338032	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57839482	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58766815	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61299530	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61388072	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72738729	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72738743	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72738757	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8036042	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041628	0.85[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs16969899	IREB2	cis	Whole Blood	GTEx
rs16969899	RASGRF1	cis	parietal	SCAN
rs16969899	CHRNA5	cis	parietal	SCAN
rs16969899	CHRNA5	cis	cerebellum	SCAN
rs16969899	IREB2	cis	multi-tissue	Pritchard
rs16969899	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	chr15:78751000-78793200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:78754000-78789400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:78754400-78787600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:78754600-78793400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:78754800-78793800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr15:78755000-78787000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr15:78755000-78787000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr15:78755000-78793800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:78755000-78794400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:78755200-78783800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr15:78755200-78787000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:78755200-78792600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr15:78755200-78793400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:78755200-78793600	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr15:78755200-78793800	Strong transcription	Fetal Thymus	thymus
17	chr15:78755200-78794000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:78755200-78794600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:78755400-78783200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr15:78755400-78791400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:78755400-78791400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr15:78755400-78791800	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr15:78755400-78792600	Strong transcription	Fetal Muscle Leg	muscle
24	chr15:78755400-78793600	Strong transcription	Liver	Liver
25	chr15:78756000-78783600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr15:78756000-78792800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr15:78756000-78793600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:78757000-78789600	Weak transcription	Stomach Mucosa	stomach
29	chr15:78759000-78793000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:78759800-78793800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr15:78760800-78787000	Weak transcription	Aorta	Aorta
32	chr15:78761800-78792000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr15:78762200-78791600	Strong transcription	Fetal Intestine Large	intestine
34	chr15:78766000-78799200	Weak transcription	Fetal Heart	heart
35	chr15:78767800-78785800	Strong transcription	Fetal Lung	lung
36	chr15:78767800-78792600	Strong transcription	Primary T cells from cord blood	blood
37	chr15:78767800-78794200	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr15:78771000-78785000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:78771000-78790200	Weak transcription	Psoas Muscle	Psoas
40	chr15:78771200-78784800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:78772400-78794600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:78773400-78786800	Strong transcription	Thymus	Thymus
43	chr15:78773800-78783600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr15:78774200-78783800	Strong transcription	HSMM	muscle
45	chr15:78774200-78785600	Strong transcription	Dnd41	blood
46	chr15:78774200-78792000	Strong transcription	Hela-S3	cervix
47	chr15:78774400-78783400	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr15:78774400-78787000	Strong transcription	A549	lung
49	chr15:78774600-78792800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:78774800-78792600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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