Variant report

Variant	rs190450
Chromosome Location	chr5:127614472-127614473
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127609023..127610896-chr5:127612305..127614881,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1086260	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs194277	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs255695	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32205	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs32216	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs364671	0.85[JPT][hapmap]
rs426987	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469750	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830482	chr5:127475398-127665377	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv599697	chr5:127563563-127731210	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv830483	chr5:127595570-127705124	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs190450	CHSY3	cis	parietal	SCAN
rs190450	PHAX	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127589000-127670200	Weak transcription	NHDF-Ad	bronchial
2	chr5:127592600-127614600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:127592800-127624400	Weak transcription	A549	lung
4	chr5:127592800-127631600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:127593800-127635200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:127596200-127623800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:127598800-127622600	Weak transcription	Fetal Intestine Large	intestine
8	chr5:127598800-127623800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:127599200-127622400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:127599200-127623000	Weak transcription	Fetal Intestine Small	intestine
11	chr5:127599400-127624200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:127599400-127624200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:127600800-127624200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:127605200-127614600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:127605200-127628800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr5:127605400-127617200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:127607000-127616600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:127607200-127616400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:127608000-127622200	Weak transcription	Fetal Lung	lung
20	chr5:127608000-127629600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:127608600-127616600	Strong transcription	Placenta	Placenta
22	chr5:127609000-127614600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:127609200-127615000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:127610800-127615600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:127611600-127614600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:127611600-127614600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:127611600-127614600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:127611600-127614600	Strong transcription	Fetal Heart	heart
29	chr5:127611600-127614800	Strong transcription	NHEK	skin
30	chr5:127611600-127616200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:127611600-127616600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr5:127611800-127614800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:127612200-127614600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr5:127612200-127614600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr5:127612200-127614600	Strong transcription	Fetal Muscle Leg	muscle
36	chr5:127612600-127615600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:127612800-127614600	Strong transcription	Fetal Stomach	stomach
38	chr5:127612800-127622200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr5:127612800-127662400	Weak transcription	HUVEC	blood vessel
40	chr5:127613400-127614600	Strong transcription	Ovary	ovary
41	chr5:127613600-127614600	Strong transcription	Fetal Kidney	kidney
42	chr5:127613600-127616600	Strong transcription	HMEC	breast
43	chr5:127613600-127623000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:127613800-127622200	Weak transcription	Left Ventricle	heart
45	chr5:127614000-127620000	Weak transcription	NH-A	brain
46	chr5:127614000-127622200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:127614000-127623400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr5:127614200-127615600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:127614400-127614600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:127614400-127622000	Weak transcription	Placenta Amnion	Placenta Amnion

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