Variant report

Variant	rs939293
Chromosome Location	chr4:57196155-57196156
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10434444	0.95[JPT][hapmap]
rs1060472	0.95[JPT][hapmap]
rs11133439	0.91[CEU][hapmap];0.85[MEX][hapmap]
rs11133442	0.90[JPT][hapmap]
rs11724302	0.84[CEU][hapmap]
rs11733474	0.84[CEU][hapmap]
rs12498340	0.95[JPT][hapmap]
rs12504291	0.94[JPT][hapmap]
rs12508008	0.85[JPT][hapmap]
rs13147900	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1401904	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1401906	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1401907	0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs14211	0.85[JPT][hapmap]
rs17086696	0.95[JPT][hapmap]
rs17086832	0.83[JPT][hapmap]
rs17086853	0.85[JPT][hapmap]
rs1967559	0.90[JPT][hapmap]
rs1983377	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1983378	0.95[JPT][hapmap]
rs2292985	0.84[CEU][hapmap];0.90[MEX][hapmap]
rs4340842	0.80[JPT][hapmap]
rs4618376	0.85[JPT][hapmap]
rs4864579	0.95[JPT][hapmap]
rs4864583	0.90[JPT][hapmap]
rs4865090	0.82[CEU][hapmap]
rs4865092	0.89[JPT][hapmap]
rs5010012	0.88[JPT][hapmap]
rs56046844	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554345	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554348	0.84[CEU][hapmap];0.85[MEX][hapmap]
rs6554358	0.85[JPT][hapmap]
rs6821301	0.90[JPT][hapmap]
rs6834736	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6849183	0.90[JPT][hapmap]
rs6854278	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7664841	0.90[JPT][hapmap]
rs7671868	0.86[TSI][hapmap]
rs7693137	0.84[CEU][hapmap];0.85[MEX][hapmap]
rs8340	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs939293	PPAT	cis	lymphoblastoid	seeQTL
rs939293	AASDH	cis	parietal	SCAN
rs939293	AASDH	cis	Skin Sun Exposed Lower leg	GTEx
rs939293	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs939293	AASDH	cis	cerebellum	SCAN
rs939293	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57167600-57203400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
3	chr4:57172000-57204000	Weak transcription	Stomach Mucosa	stomach
4	chr4:57173200-57202800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:57174400-57203800	Weak transcription	Fetal Kidney	kidney
6	chr4:57174600-57197200	Strong transcription	Duodenum Mucosa	Duodenum
7	chr4:57177600-57215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:57178200-57211800	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:57180800-57197200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:57181200-57196400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:57181400-57203800	Weak transcription	HSMMtube	muscle
12	chr4:57181800-57196200	Strong transcription	Fetal Intestine Large	intestine
13	chr4:57182800-57196800	Weak transcription	Ovary	ovary
14	chr4:57184600-57211200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:57187200-57202600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:57188400-57203600	Weak transcription	Fetal Lung	lung
17	chr4:57188600-57197800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:57190400-57203000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:57190400-57203200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:57190400-57203600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr4:57190400-57214400	Weak transcription	Brain Anterior Caudate	brain
22	chr4:57190600-57214600	Weak transcription	Brain Substantia Nigra	brain
23	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
24	chr4:57190800-57196400	Weak transcription	Fetal Muscle Leg	muscle
25	chr4:57190800-57197000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:57190800-57202600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr4:57190800-57202600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:57190800-57203200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:57190800-57203600	Weak transcription	Fetal Brain Male	brain
30	chr4:57190800-57203800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:57191000-57204000	Weak transcription	Brain Angular Gyrus	brain
32	chr4:57192600-57197200	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr4:57192800-57197000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:57193000-57204000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:57193600-57213000	Weak transcription	Left Ventricle	heart
36	chr4:57193800-57196400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:57193800-57196400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:57194800-57202600	Weak transcription	Fetal Stomach	stomach
39	chr4:57194800-57203000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr4:57195000-57202600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:57195000-57202600	Weak transcription	Fetal Intestine Small	intestine
42	chr4:57195000-57214400	Weak transcription	Placenta	Placenta
43	chr4:57195200-57238000	Weak transcription	HUVEC	blood vessel
44	chr4:57195400-57203200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:57195600-57196800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:57195800-57196600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr4:57195800-57203000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:57195800-57203000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:57195800-57203000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:57195800-57203000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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