Variant report

Variant	rs16969407
Chromosome Location	chr15:78310043-78310044
allele	C/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	GATA3	chr15:78309979-78310179	SH-SY5Y	brain:	n/a	chr15:78310062-78310078 chr15:78310066-78310075 chr15:78309988-78310005
2	GATA1	chr15:78310001-78310425	PBDE	blood:	n/a	chr15:78310062-78310078 chr15:78310066-78310075

Variant related genes	Relation type
TBC1D2B	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10519182	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11629761	0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs11639164	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs11854491	0.87[AMR][1000 genomes]
rs12102130	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13329101	0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13329302	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16969367	1.00[ASW][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs16969405	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16969408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16969414	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16969423	1.00[ASW][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs16969424	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16969430	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16969447	1.00[MEX][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs1985487	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28394000	0.89[AFR][1000 genomes]
rs28417785	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28441175	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28451835	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28470811	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28485414	0.81[AFR][1000 genomes]
rs28491609	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs28491820	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28519575	0.89[AFR][1000 genomes]
rs28526757	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28579273	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28581571	0.96[AFR][1000 genomes]
rs28590577	0.83[AFR][1000 genomes]
rs28591625	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28647720	0.96[AFR][1000 genomes]
rs28674965	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4991997	0.88[EUR][1000 genomes]
rs55663439	0.88[EUR][1000 genomes]
rs55930913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58098690	0.88[EUR][1000 genomes]
rs58117418	0.88[EUR][1000 genomes]
rs58247186	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7167778	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74027705	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74027706	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74027709	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74029743	0.88[EUR][1000 genomes]
rs74029754	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7495639	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9920647	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78284600-78310200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr15:78286000-78310400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr15:78287000-78316000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:78288400-78311000	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr15:78288800-78310400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr15:78296200-78316400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:78297400-78310800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:78297600-78310400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:78300600-78316400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:78300800-78315400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:78301000-78310200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:78301000-78311400	Weak transcription	Right Atrium	heart
14	chr15:78301000-78316400	Weak transcription	Psoas Muscle	Psoas
15	chr15:78301200-78315800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:78301400-78342200	Weak transcription	HMEC	breast
17	chr15:78301800-78313800	Strong transcription	Fetal Muscle Leg	muscle
18	chr15:78302200-78315400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr15:78302800-78310400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:78303200-78342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:78304800-78310600	Strong transcription	NHDF-Ad	bronchial
22	chr15:78305000-78310200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr15:78305200-78310400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:78305400-78311200	Weak transcription	K562	blood
25	chr15:78305400-78315400	Strong transcription	Placenta	Placenta
26	chr15:78305400-78317600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:78305400-78329800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:78305600-78310200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:78305600-78310200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr15:78305600-78312600	Weak transcription	Fetal Brain Male	brain
31	chr15:78305600-78315600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:78305600-78325800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr15:78306000-78310200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr15:78306400-78310400	Strong transcription	Fetal Intestine Large	intestine
35	chr15:78306800-78312600	Weak transcription	Stomach Mucosa	stomach
36	chr15:78307200-78342000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:78308400-78312600	Weak transcription	HUVEC	blood vessel
38	chr15:78308600-78315200	Weak transcription	Hela-S3	cervix
39	chr15:78308800-78312400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:78308800-78315400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:78308800-78315600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr15:78308800-78315800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:78308800-78327200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:78309000-78311400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr15:78309000-78311400	Weak transcription	Colonic Mucosa	Colon
46	chr15:78309000-78312600	Weak transcription	Brain Hippocampus Middle	brain
47	chr15:78309000-78312600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:78309000-78313000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:78309000-78313800	Weak transcription	Aorta	Aorta
50	chr15:78309000-78315200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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