Variant report

Variant	rs17314168
Chromosome Location	chr3:139350316-139350317
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	chr3:139345093..139348076-chr3:139348781..139350988,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10935340	1.00[YRI][hapmap]
rs12492528	1.00[YRI][hapmap]
rs12635533	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs188423	0.84[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap]
rs2291803	1.00[YRI][hapmap]
rs295464	0.84[ASW][hapmap];0.96[MKK][hapmap]
rs295507	0.84[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap]
rs454481	0.84[ASW][hapmap];0.95[MKK][hapmap]
rs47442	0.91[MKK][hapmap]
rs62273065	0.90[EUR][1000 genomes]
rs62273066	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62273067	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9790066	1.00[YRI][hapmap]
rs9873488	0.96[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17314168	ESYT3	cis	parietal	SCAN
rs17314168	SOX14	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139291600-139352400	Weak transcription	Fetal Intestine Small	intestine
2	chr3:139317200-139352400	Weak transcription	Pancreas	Pancrea
3	chr3:139317600-139352400	Weak transcription	Left Ventricle	heart
4	chr3:139317800-139360200	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:139318200-139352400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:139329800-139362400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:139331000-139355800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:139332000-139352400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:139333600-139352200	Weak transcription	Ovary	ovary
10	chr3:139334800-139352400	Weak transcription	Esophagus	oesophagus
11	chr3:139336400-139351400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:139338600-139360000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:139344000-139360200	Weak transcription	Right Ventricle	heart
14	chr3:139344800-139352400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:139344800-139355200	Weak transcription	Adipose Nuclei	Adipose
16	chr3:139346600-139351200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:139346800-139352400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:139346800-139355000	Weak transcription	Fetal Intestine Large	intestine
19	chr3:139346800-139361200	Weak transcription	Spleen	Spleen
20	chr3:139347000-139358000	Weak transcription	Fetal Brain Female	brain
21	chr3:139347200-139360200	Weak transcription	Right Atrium	heart
22	chr3:139348200-139352600	Weak transcription	Fetal Stomach	stomach
23	chr3:139348200-139355600	Weak transcription	Gastric	stomach
24	chr3:139348400-139353000	Weak transcription	Lung	lung
25	chr3:139348600-139352800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:139348600-139359400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:139348800-139350400	Enhancers	Cortex derived primary cultured neurospheres	brain

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