Variant report

Variant	rs11733474
Chromosome Location	chr4:57194329-57194330
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10015221	0.89[JPT][hapmap]
rs10015634	0.89[JPT][hapmap]
rs10031550	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10034154	0.80[ASN][1000 genomes]
rs10518	0.89[JPT][hapmap]
rs10866433	0.89[JPT][hapmap]
rs11133438	0.86[EUR][1000 genomes]
rs11133439	1.00[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs11724302	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12331363	0.90[ASN][1000 genomes]
rs12331412	0.89[ASN][1000 genomes]
rs13114104	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13138648	0.89[EUR][1000 genomes]
rs13141793	0.83[CEU][hapmap];0.90[TSI][hapmap]
rs13147824	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13147900	0.81[CEU][hapmap]
rs1356788	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1401904	0.81[CEU][hapmap]
rs1401912	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1464286	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17051687	0.89[JPT][hapmap]
rs17086803	0.89[JPT][hapmap]
rs1976815	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1996650	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2030362	0.87[EUR][1000 genomes]
rs2030365	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2049087	0.94[JPT][hapmap]
rs2139512	0.87[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2292985	1.00[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs28559894	0.85[ASN][1000 genomes]
rs2899063	0.81[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796542	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3796547	0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs3822003	0.90[CHD][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs4073691	0.94[JPT][hapmap]
rs4167	0.81[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4305581	0.94[JPT][hapmap]
rs4864581	0.87[EUR][1000 genomes]
rs4865087	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865090	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4865100	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4865101	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57503982	0.92[ASN][1000 genomes]
rs59615456	0.83[ASN][1000 genomes]
rs61750793	0.82[ASN][1000 genomes]
rs62310633	0.84[ASN][1000 genomes]
rs6554345	0.88[CEU][hapmap]
rs6554348	1.00[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs6554349	0.87[CEU][hapmap]
rs6554352	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554355	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6554356	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6811821	0.89[JPT][hapmap]
rs6812041	0.86[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6819534	0.94[JPT][hapmap]
rs6826795	0.87[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6834736	0.88[CEU][hapmap]
rs6836864	0.92[EUR][1000 genomes]
rs6841053	0.91[ASN][1000 genomes]
rs6856845	0.85[EUR][1000 genomes]
rs73240541	0.84[ASN][1000 genomes]
rs7657711	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7661712	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7683781	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7692385	0.87[CEU][hapmap]
rs7693137	1.00[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs7700034	0.84[JPT][hapmap]
rs9312673	0.81[EUR][1000 genomes]
rs9312674	0.87[ASN][1000 genomes]
rs9683679	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9684298	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9996593	0.89[JPT][hapmap]
rs9997639	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11733474	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs11733474	PPAT	cis	lymphoblastoid	seeQTL
rs11733474	AASDH	cis	parietal	SCAN
rs11733474	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 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	chr4:57174400-57195000	Strong transcription	Fetal Intestine Small	intestine
6	chr4:57174400-57203800	Weak transcription	Fetal Kidney	kidney
7	chr4:57174600-57197200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr4:57177600-57215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:57178200-57211800	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:57180800-57197200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:57181200-57196400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:57181400-57203800	Weak transcription	HSMMtube	muscle
13	chr4:57181800-57196200	Strong transcription	Fetal Intestine Large	intestine
14	chr4:57182800-57196800	Weak transcription	Ovary	ovary
15	chr4:57183200-57194400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:57184600-57211200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:57187200-57202600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:57188400-57203600	Weak transcription	Fetal Lung	lung
19	chr4:57188600-57197800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:57189000-57195800	Strong transcription	Brain Germinal Matrix	brain
21	chr4:57189400-57195800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr4:57190400-57203000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr4:57190400-57203200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr4:57190400-57203600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:57190400-57214400	Weak transcription	Brain Anterior Caudate	brain
26	chr4:57190600-57214600	Weak transcription	Brain Substantia Nigra	brain
27	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
28	chr4:57190800-57194400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:57190800-57194600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:57190800-57196400	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:57190800-57197000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:57190800-57202600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:57190800-57202600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:57190800-57203200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr4:57190800-57203600	Weak transcription	Fetal Brain Male	brain
36	chr4:57190800-57203800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:57191000-57204000	Weak transcription	Brain Angular Gyrus	brain
38	chr4:57192200-57195400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:57192600-57197200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr4:57192800-57194800	Weak transcription	HUVEC	blood vessel
41	chr4:57192800-57197000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:57193000-57204000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:57193200-57195600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:57193200-57196000	Strong transcription	Fetal Brain Female	brain
45	chr4:57193600-57196000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:57193600-57213000	Weak transcription	Left Ventricle	heart
47	chr4:57193800-57194800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:57193800-57194800	Strong transcription	Fetal Stomach	stomach
49	chr4:57193800-57195000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:57193800-57195800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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