Variant report

Variant	rs1541160
Chromosome Location	chr1:169995802-169995803
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10489172	0.93[MEX][hapmap]
rs10494482	1.00[CHB][hapmap]
rs1062976	0.93[MEX][hapmap]
rs10919283	0.93[YRI][hapmap]
rs11584929	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589247	0.86[YRI][hapmap]
rs12089836	1.00[CHB][hapmap]
rs12760399	0.92[MEX][hapmap]
rs1330377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16862745	0.86[YRI][hapmap]
rs16863058	1.00[CHB][hapmap]
rs2050628	0.93[YRI][hapmap]
rs2065950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2474708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28441321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476269	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516793	0.85[MEX][hapmap]
rs522444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527261	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541655	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546894	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549002	0.84[AFR][1000 genomes]
rs571398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574053	1.00[CHB][hapmap];0.91[MKK][hapmap]
rs614044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621437	0.85[MEX][hapmap]
rs628436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427230	0.93[YRI][hapmap]
rs6427232	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648576	0.91[ASW][hapmap];0.81[CEU][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6668310	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676005	1.00[CHB][hapmap]
rs6694304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693673	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715936	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7354853	1.00[CHB][hapmap]
rs7354854	1.00[CHB][hapmap]
rs7539241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427175	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973015	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Amyotrophic lateral sclerosis	19451621	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1541160	ALDH9A1	cis	parietal	SCAN
rs1541160	BLZF1	cis	parietal	SCAN
rs1541160	C1orf112	cis	cerebellum	SCAN
rs1541160	C1orf156	cis	lymphoblastoid	seeQTL
rs1541160	KIFAP3	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169904000-170010400	Weak transcription	Aorta	Aorta
2	chr1:169922400-169996400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:169951600-170011800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:169952000-170018000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:169952400-170043000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:169956800-169997400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:169967600-170013000	Weak transcription	Fetal Heart	heart
8	chr1:169968800-169999400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:169968800-170010800	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:169968800-170020200	Weak transcription	Brain Angular Gyrus	brain
11	chr1:169969000-169997400	Weak transcription	Fetal Stomach	stomach
12	chr1:169969000-170012600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:169969600-170017800	Weak transcription	Esophagus	oesophagus
14	chr1:169971400-169996400	Weak transcription	NHDF-Ad	bronchial
15	chr1:169979400-170018000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:169979800-170015200	Weak transcription	HMEC	breast
17	chr1:169980000-170006600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:169980600-169997400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:169981600-170013400	Weak transcription	Lung	lung
20	chr1:169982400-170020600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:169983000-170017200	Weak transcription	HSMMtube	muscle
22	chr1:169983400-169996000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr1:169983800-170017600	Weak transcription	Spleen	Spleen
24	chr1:169984600-170020800	Weak transcription	Gastric	stomach
25	chr1:169984800-170027600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:169985000-169996600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:169985000-170010800	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:169985000-170012800	Weak transcription	Brain Anterior Caudate	brain
29	chr1:169985200-169997000	Weak transcription	Primary B cells from cord blood	blood
30	chr1:169985200-170020400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:169985800-169996400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:169985800-170003000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:169985800-170010800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:169985800-170010800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:169986000-169996600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr1:169986200-169996000	Weak transcription	Fetal Intestine Large	intestine
37	chr1:169986200-169996200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:169986200-169996400	Weak transcription	Adipose Nuclei	Adipose
39	chr1:169986200-169996600	Weak transcription	Primary T cells from cord blood	blood
40	chr1:169986200-170006600	Weak transcription	Ovary	ovary
41	chr1:169986200-170010600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:169986400-169996200	Weak transcription	Fetal Thymus	thymus
43	chr1:169986400-170013600	Weak transcription	Left Ventricle	heart
44	chr1:169986400-170019800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:169988000-170001200	Weak transcription	Osteobl	bone
46	chr1:169988000-170017600	Weak transcription	Fetal Lung	lung
47	chr1:169989200-170006400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:169989600-170019800	Weak transcription	Right Ventricle	heart
49	chr1:169989800-169996200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:169989800-170013400	Weak transcription	Psoas Muscle	Psoas

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