Variant report

Variant	rs32216
Chromosome Location	chr5:127640076-127640077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1086260	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs190450	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]
rs194277	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs255695	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs32205	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs32206	0.80[TSI][hapmap]
rs364671	0.85[JPT][hapmap];0.83[YRI][hapmap]
rs426987	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs469750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs32216	CHSY3	cis	parietal	SCAN
rs32216	PHAX	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127589000-127670200	Weak transcription	NHDF-Ad	bronchial
2	chr5:127612800-127662400	Weak transcription	HUVEC	blood vessel
3	chr5:127614600-127644800	Weak transcription	Ovary	ovary
4	chr5:127614600-127661000	Weak transcription	Fetal Kidney	kidney
5	chr5:127622800-127662000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:127624600-127663600	Weak transcription	A549	lung
7	chr5:127624800-127644000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:127624800-127648000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:127625000-127662200	Weak transcription	Fetal Intestine Large	intestine
10	chr5:127626000-127664400	Weak transcription	Right Ventricle	heart
11	chr5:127626200-127640400	Weak transcription	Left Ventricle	heart
12	chr5:127626600-127664200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:127634400-127656200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:127635000-127641800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:127635200-127646600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr5:127635600-127645600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:127635600-127654800	Strong transcription	Placenta	Placenta
18	chr5:127635800-127641600	Strong transcription	HMEC	breast
19	chr5:127636200-127648000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:127636200-127648800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr5:127636600-127642800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:127636600-127643800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:127636600-127661800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr5:127636800-127640200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:127636800-127644800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:127636800-127647800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:127637400-127640200	Weak transcription	NHLF	lung
28	chr5:127637600-127641600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:127637600-127641600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:127638200-127645800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:127638200-127685000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:127638400-127641000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:127638600-127644000	Weak transcription	Fetal Heart	heart
34	chr5:127638800-127640400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:127639000-127640200	Enhancers	NHEK	skin
36	chr5:127639000-127640600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:127639200-127640200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:127639400-127640200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr5:127639400-127641000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr5:127639600-127640200	Enhancers	Fetal Stomach	stomach
41	chr5:127639600-127640400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:127639600-127640600	Genic enhancers	Muscle Satellite Cultured Cells	--
43	chr5:127639600-127640600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:127639600-127640600	Weak transcription	HSMMtube	muscle
45	chr5:127639600-127641400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:127639600-127641400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:127639600-127642600	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr5:127639800-127640200	Weak transcription	Fetal Muscle Leg	muscle
49	chr5:127639800-127640600	Enhancers	NH-A	brain
50	chr5:127640000-127641000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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