Variant report

Variant	rs8340
Chromosome Location	chr4:57204777-57204778
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10008223	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10010544	0.91[EUR][1000 genomes]
rs10013402	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10017460	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10434444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10434445	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10461357	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1060472	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11133442	0.83[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.81[ASN][1000 genomes]
rs11133443	1.00[CEU][hapmap];0.89[TSI][hapmap]
rs1124569	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11723782	0.91[EUR][1000 genomes]
rs12498340	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12501334	0.89[ASN][1000 genomes]
rs12501502	0.81[LWK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap]
rs12503412	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12504291	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs12508008	0.95[CHD][hapmap];0.91[GIH][hapmap]
rs12512742	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12646703	0.80[MEX][hapmap]
rs13147900	0.90[JPT][hapmap]
rs1356787	0.80[MEX][hapmap]
rs1401904	0.90[JPT][hapmap]
rs1401906	0.90[JPT][hapmap];0.84[YRI][hapmap]
rs14211	0.95[CHD][hapmap];0.91[GIH][hapmap]
rs1474179	0.84[ASN][1000 genomes]
rs1520026	0.83[TSI][hapmap]
rs1520030	0.81[YRI][hapmap]
rs17086696	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17086794	0.81[ASN][1000 genomes]
rs17086853	0.95[CHD][hapmap];0.91[GIH][hapmap]
rs1967559	0.83[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs1983378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2030366	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2049088	0.90[EUR][1000 genomes]
rs2271923	0.81[LWK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap]
rs2271925	0.84[EUR][1000 genomes]
rs28510634	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28866881	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3796548	1.00[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs3822001	1.00[CEU][hapmap]
rs4263445	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4340842	0.95[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs4493603	0.83[TSI][hapmap];0.81[YRI][hapmap]
rs4864579	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4864580	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4864583	1.00[CHB][hapmap];0.90[YRI][hapmap];0.89[ASN][1000 genomes]
rs4865088	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865089	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4865092	1.00[CEU][hapmap];0.90[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5010012	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs56066795	0.84[EUR][1000 genomes]
rs56392224	0.89[ASN][1000 genomes]
rs56887793	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58151706	0.88[ASN][1000 genomes]
rs59997251	0.87[EUR][1000 genomes]
rs61032900	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554344	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs6554345	0.90[JPT][hapmap]
rs6554358	0.86[CHD][hapmap];0.91[GIH][hapmap]
rs6584	0.80[MEX][hapmap]
rs66858948	0.81[ASN][1000 genomes]
rs67957495	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6820279	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6820314	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6821301	0.91[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs6829250	0.89[ASN][1000 genomes]
rs6830518	0.80[MEX][hapmap]
rs6832797	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6834696	0.91[ASN][1000 genomes]
rs6834736	0.90[JPT][hapmap]
rs6836118	1.00[CEU][hapmap];0.89[TSI][hapmap]
rs6849183	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs7664841	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.82[ASN][1000 genomes]
rs7670991	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7696808	1.00[CEU][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.93[EUR][1000 genomes]
rs9799864	0.82[AMR][1000 genomes];0.87[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8340	AASDH	cis	cerebellum	SCAN
rs8340	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs8340	SRP72	cis	normal skin	skin_eQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
2	chr4:57177600-57215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:57178200-57211800	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:57184600-57211200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:57190400-57214400	Weak transcription	Brain Anterior Caudate	brain
6	chr4:57190600-57214600	Weak transcription	Brain Substantia Nigra	brain
7	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
8	chr4:57193600-57213000	Weak transcription	Left Ventricle	heart
9	chr4:57195000-57214400	Weak transcription	Placenta	Placenta
10	chr4:57195200-57238000	Weak transcription	HUVEC	blood vessel
11	chr4:57196000-57238200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:57198800-57214400	Weak transcription	Gastric	stomach
13	chr4:57201800-57212000	Weak transcription	Adipose Nuclei	Adipose
14	chr4:57202000-57212000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr4:57202400-57204800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:57202600-57204800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:57202600-57204800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:57202600-57205000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
19	chr4:57202600-57205000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
20	chr4:57202600-57205000	Strong transcription	Fetal Intestine Large	intestine
21	chr4:57202600-57221400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:57202800-57204800	Strong transcription	Duodenum Mucosa	Duodenum
23	chr4:57202800-57204800	Strong transcription	Fetal Brain Female	brain
24	chr4:57202800-57205200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
25	chr4:57202800-57252400	Weak transcription	NHDF-Ad	bronchial
26	chr4:57203000-57204800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:57203000-57205000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr4:57203000-57205200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
29	chr4:57203000-57205200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:57203000-57205200	Strong transcription	Brain Germinal Matrix	brain
31	chr4:57203000-57252600	Weak transcription	Right Ventricle	heart
32	chr4:57203200-57204800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr4:57203200-57204800	Strong transcription	Fetal Stomach	stomach
34	chr4:57203200-57204800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr4:57203200-57205000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
36	chr4:57203200-57205000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:57203200-57215000	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:57203200-57215600	Weak transcription	Pancreas	Pancrea
39	chr4:57203200-57235200	Weak transcription	Osteobl	bone
40	chr4:57203200-57251800	Weak transcription	A549	lung
41	chr4:57203400-57205000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:57203400-57205200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:57203400-57212800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:57203400-57252400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr4:57203600-57204800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:57203600-57204800	Strong transcription	Fetal Brain Male	brain
47	chr4:57203600-57204800	Strong transcription	Psoas Muscle	Psoas
48	chr4:57203600-57205000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
49	chr4:57203600-57205200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:57203600-57205200	Strong transcription	Brain Inferior Temporal Lobe	brain

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