Variant report

Variant	rs2235195
Chromosome Location	chr1:169396620-169396621
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10158131	0.82[CEU][hapmap];0.86[MEX][hapmap]
rs10489187	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489188	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800439	0.86[CHB][hapmap]
rs10800441	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs10919140	0.86[MEX][hapmap]
rs10919146	0.88[EUR][1000 genomes]
rs10919155	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919163	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11799936	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11799948	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11800843	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11808015	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11808274	0.89[JPT][hapmap];0.83[YRI][hapmap]
rs11809378	0.93[EUR][1000 genomes]
rs12021770	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12022776	0.80[ASN][1000 genomes]
rs12023025	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023117	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023892	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12024897	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs12026728	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12026996	0.80[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12028813	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12029853	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs12030320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12032201	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12033253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12037211	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap]
rs12038609	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap]
rs12043489	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap]
rs12046139	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs12049227	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12239720	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12563090	0.83[CHD][hapmap]
rs1400838	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1415928	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1589113	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16828170	0.89[JPT][hapmap];0.83[YRI][hapmap]
rs16862118	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16862172	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862199	0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs1980198	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs2268048	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[YRI][hapmap]
rs2275299	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs28566091	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35269183	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737682	0.85[CHB][hapmap]
rs3766089	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[YRI][hapmap]
rs3818844	0.86[CHB][hapmap]
rs4656670	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs56859218	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61807018	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61808977	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61808978	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61808980	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6427191	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6656923	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6669741	0.85[CHB][hapmap]
rs6677410	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs6690801	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696810	0.86[CHB][hapmap];0.83[CHD][hapmap];0.80[ASN][1000 genomes]
rs72702156	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72702179	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72702188	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7516248	0.80[ASN][1000 genomes]
rs7534737	0.86[CHB][hapmap]
rs7535788	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7537890	0.80[ASN][1000 genomes]
rs7539415	0.86[CHB][hapmap]
rs7554703	0.97[ASN][1000 genomes]
rs961404	0.80[ASN][1000 genomes]
rs9659035	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2235195	FMO9P	cis	parietal	SCAN
rs2235195	SCYL3	cis	parietal	SCAN
rs2235195	C1orf114	cis	cerebellum	SCAN
rs2235195	NME7	cis	parietal	SCAN
rs2235195	F5	cis	cerebellum	SCAN
rs2235195	C1orf114	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169394800-169397200	Active TSS	Brain Germinal Matrix	brain
2	chr1:169394800-169397200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr1:169395200-169397200	Active TSS	Brain Angular Gyrus	brain
4	chr1:169395200-169397200	Active TSS	Brain Cingulate Gyrus	brain
5	chr1:169395200-169397200	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr1:169395200-169397200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:169395400-169397200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:169395400-169397200	Active TSS	Brain Hippocampus Middle	brain
9	chr1:169395400-169397200	Active TSS	Brain Substantia Nigra	brain
10	chr1:169395400-169397200	Active TSS	Fetal Brain Female	brain
11	chr1:169395400-169397200	Active TSS	Ovary	ovary
12	chr1:169395400-169397200	Active TSS	Right Atrium	heart
13	chr1:169395400-169397200	Active TSS	NHLF	lung
14	chr1:169395600-169396800	Active TSS	NH-A	brain
15	chr1:169395600-169397200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:169395600-169397200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:169395600-169397200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:169395600-169397200	Active TSS	Fetal Brain Male	brain
19	chr1:169395600-169397200	Active TSS	Fetal Kidney	kidney
20	chr1:169395800-169396800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:169395800-169397000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr1:169395800-169397000	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr1:169395800-169397200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:169396000-169397200	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr1:169396000-169397200	Active TSS	H1 Cell Line	embryonic stem cell
26	chr1:169396000-169397200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:169396000-169397200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:169396000-169397200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr1:169396000-169397200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:169396000-169397200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:169396000-169397200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:169396000-169397200	Active TSS	HSMMtube	muscle
33	chr1:169396000-169397400	Active TSS	Brain Anterior Caudate	brain
34	chr1:169396000-169397400	Flanking Active TSS	Dnd41	blood
35	chr1:169396200-169396800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr1:169396200-169396800	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
37	chr1:169396200-169396800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
38	chr1:169396200-169396800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
39	chr1:169396200-169396800	Flanking Active TSS	Fetal Muscle Trunk	muscle
40	chr1:169396200-169396800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
41	chr1:169396200-169396800	Bivalent/Poised TSS	Osteobl	bone
42	chr1:169396200-169397000	Active TSS	H9 Cell Line	embryonic stem cell
43	chr1:169396200-169397000	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr1:169396200-169397000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:169396200-169397000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:169396200-169397000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:169396200-169397000	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr1:169396200-169397000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
49	chr1:169396200-169397000	Active TSS	Aorta	Aorta
50	chr1:169396200-169397000	Active TSS	Fetal Heart	heart

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