Variant report

Variant	rs1464517
Chromosome Location	chr3:150342895-150342896
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:150342865-150343296	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150340005..150343317-chr3:150348325..150351775,4	K562	blood:
2	chr3:150320987..150322498-chr3:150342766..150344939,2	K562	blood:
3	chr3:150341447..150343968-chr3:150345071..150346615,2	K562	blood:
4	chr3:150341329..150343793-chr3:150348325..150350105,2	K562	blood:
5	chr3:150258291..150260561-chr3:150340195..150342969,2	K562	blood:
6	chr3:150320191..150322679-chr3:150341906..150344166,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198843	TF binding region
ENSG00000198843	Chromatin interaction
ENSG00000120742	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1133494	0.81[ASW][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap]
rs13097283	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1915943	0.86[LWK][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2049229	0.88[CEU][hapmap];0.81[LWK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[EUR][1000 genomes]
rs2204112	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2868947	0.93[EUR][1000 genomes]
rs4681636	1.00[CHB][hapmap]
rs6790726	0.82[YRI][hapmap]
rs6798173	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6801796	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6802114	1.00[CHB][hapmap]
rs7433606	0.94[ASW][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7638500	0.81[ASW][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs7642917	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs9809820	0.87[LWK][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9819287	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9836797	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9874800	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	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv967272	chr3:150340723-150348299	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1464517	EIF2A	cis	Artery Tibial	GTEx
rs1464517	TM4SF4	cis	parietal	SCAN
rs1464517	COMMD2	cis	cerebellum	SCAN
rs1464517	EIF2A	cis	Frontal Cortex	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150322200-150347000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:150322400-150344000	Weak transcription	HSMMtube	muscle
3	chr3:150322400-150350800	Weak transcription	Colonic Mucosa	Colon
4	chr3:150322400-150353000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:150323000-150343800	Weak transcription	HMEC	breast
6	chr3:150323000-150348200	Weak transcription	Fetal Brain Male	brain
7	chr3:150323000-150348200	Weak transcription	Fetal Lung	lung
8	chr3:150325600-150348400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:150325800-150344200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:150326000-150343800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:150326000-150348400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:150326000-150352800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:150326600-150343800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:150326800-150343000	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:150326800-150344200	Weak transcription	Fetal Brain Female	brain
16	chr3:150327400-150343200	Weak transcription	Left Ventricle	heart
17	chr3:150327600-150343800	Weak transcription	Small Intestine	intestine
18	chr3:150328200-150343800	Weak transcription	Aorta	Aorta
19	chr3:150328600-150344200	Weak transcription	Fetal Heart	heart
20	chr3:150328800-150343000	Weak transcription	Brain Anterior Caudate	brain
21	chr3:150328800-150343600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:150328800-150343800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:150329800-150343600	Weak transcription	Pancreas	Pancrea
24	chr3:150329800-150344200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:150330000-150343000	Weak transcription	Thymus	Thymus
26	chr3:150330000-150343200	Weak transcription	Spleen	Spleen
27	chr3:150330000-150343800	Weak transcription	Lung	lung
28	chr3:150330000-150348800	Weak transcription	Right Ventricle	heart
29	chr3:150330000-150356600	Weak transcription	Gastric	stomach
30	chr3:150330200-150343000	Weak transcription	Fetal Intestine Large	intestine
31	chr3:150330200-150343800	Weak transcription	Esophagus	oesophagus
32	chr3:150330200-150343800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:150330200-150348800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:150330200-150353000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:150330400-150348400	Weak transcription	Fetal Stomach	stomach
36	chr3:150331200-150343200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:150331200-150348800	Weak transcription	Fetal Intestine Small	intestine
38	chr3:150331800-150343000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:150332000-150343200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:150332000-150348600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:150332200-150343000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:150332200-150343400	Weak transcription	K562	blood
43	chr3:150334800-150352800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:150335000-150343800	Weak transcription	Brain Germinal Matrix	brain
45	chr3:150335000-150344000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:150335800-150344000	Weak transcription	Ovary	ovary
47	chr3:150336600-150343000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:150336600-150351200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:150336800-150343000	Weak transcription	GM12878-XiMat	blood
50	chr3:150336800-150343600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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