Variant report

Variant	rs8030999
Chromosome Location	chr15:78311343-78311344
allele	A/G
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	SPI1	chr15:78311325-78311593	GM12891	blood:	n/a	n/a
2	SPI1	chr15:78311320-78311622	HL-60	blood:	n/a	n/a
3	EP300	chr15:78311296-78311774	GM12878	blood:	n/a	chr15:78311518-78311532
4	GATA1	chr15:78311037-78311806	PBDE	blood:	n/a	chr15:78311464-78311473
5	BHLHE40	chr15:78311310-78311689	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:78311263-78311928	HL-60	blood:	n/a	n/a
7	MAX	chr15:78311296-78311780	NB4	blood:	n/a	n/a
8	EP300	chr15:78311267-78311366	K562	blood:	n/a	chr15:78311287-78311301
9	SPI1	chr15:78311270-78311964	HL-60	blood:	n/a	n/a
10	SPI1	chr15:78311312-78311700	GM12891	blood:	n/a	n/a
11	RUNX3	chr15:78311187-78311766	GM12878	blood:	n/a	n/a
12	EBF1	chr15:78311216-78311809	GM12878	blood:	n/a	chr15:78311436-78311447 chr15:78311437-78311447 chr15:78311438-78311447
13	POLR2A	chr15:78311225-78311783	HL-60	blood:	n/a	n/a
14	MYC	chr15:78311320-78311851	NB4	blood:	n/a	n/a
15	EBF1	chr15:78311249-78311626	GM12878	blood:	n/a	chr15:78311436-78311447 chr15:78311437-78311447 chr15:78311438-78311447
16	SPI1	chr15:78311317-78311697	GM12878	blood:	n/a	n/a
17	EP300	chr15:78311298-78311748	GM12878	blood:	n/a	chr15:78311518-78311532
18	RUNX3	chr15:78311273-78311685	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TBC1D2B	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11631578	0.86[YRI][hapmap]
rs11634607	0.94[ASW][hapmap];0.84[LWK][hapmap];0.80[AFR][1000 genomes]
rs11858138	0.92[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs12591418	0.94[ASW][hapmap];0.84[LWK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs12594823	0.94[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs12900731	0.82[ASW][hapmap]
rs12907814	0.81[AFR][1000 genomes]
rs16953970	1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[ASN][1000 genomes]
rs16969397	0.93[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs16969464	0.87[CHB][hapmap];0.96[CHD][hapmap]
rs1837912	0.82[ASW][hapmap]
rs1992470	0.96[YRI][hapmap]
rs4886554	0.94[ASW][hapmap];0.84[LWK][hapmap];0.86[YRI][hapmap]
rs57993009	0.95[ASN][1000 genomes]
rs59499270	0.90[ASN][1000 genomes]
rs61183047	0.95[ASN][1000 genomes]
rs7170101	0.82[ASW][hapmap]
rs7170746	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs735663	0.87[CHB][hapmap]
rs8033216	0.82[ASW][hapmap]
rs9920180	0.82[ASW][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	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	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8030999	TBC1D2B	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78287000-78316000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr15:78296200-78316400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:78300600-78316400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:78300800-78315400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:78301000-78311400	Weak transcription	Right Atrium	heart
7	chr15:78301000-78316400	Weak transcription	Psoas Muscle	Psoas
8	chr15:78301200-78315800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:78301400-78342200	Weak transcription	HMEC	breast
10	chr15:78301800-78313800	Strong transcription	Fetal Muscle Leg	muscle
11	chr15:78302200-78315400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr15:78303200-78342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:78305400-78315400	Strong transcription	Placenta	Placenta
14	chr15:78305400-78317600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:78305400-78329800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:78305600-78312600	Weak transcription	Fetal Brain Male	brain
17	chr15:78305600-78315600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr15:78305600-78325800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr15:78306800-78312600	Weak transcription	Stomach Mucosa	stomach
20	chr15:78307200-78342000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:78308400-78312600	Weak transcription	HUVEC	blood vessel
22	chr15:78308600-78315200	Weak transcription	Hela-S3	cervix
23	chr15:78308800-78312400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:78308800-78315400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:78308800-78315600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:78308800-78315800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:78308800-78327200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:78309000-78311400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr15:78309000-78311400	Weak transcription	Colonic Mucosa	Colon
30	chr15:78309000-78312600	Weak transcription	Brain Hippocampus Middle	brain
31	chr15:78309000-78312600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:78309000-78313000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:78309000-78313800	Weak transcription	Aorta	Aorta
34	chr15:78309000-78315200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr15:78309000-78315400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:78309000-78315800	Weak transcription	Brain Substantia Nigra	brain
37	chr15:78309000-78316400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr15:78309000-78316400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:78309000-78317200	Weak transcription	Small Intestine	intestine
40	chr15:78309200-78312600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:78309200-78312600	Weak transcription	Colon Smooth Muscle	Colon
42	chr15:78309200-78312600	Weak transcription	Ovary	ovary
43	chr15:78309200-78312800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr15:78309200-78314000	Weak transcription	Brain Germinal Matrix	brain
45	chr15:78309200-78330200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr15:78309200-78330800	Weak transcription	A549	lung
47	chr15:78309200-78354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr15:78309400-78312200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:78309400-78312400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:78309400-78312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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