Variant report

Variant	rs1520231
Chromosome Location	chr16:65076644-65076645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:65076587..65078902-chr16:65080477..65083280,2	K562	blood:

Extended variants
information (count: 153 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs1025311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1040270	0.86[JPT][hapmap]
rs1040271	0.93[JPT][hapmap]
rs10500508	0.82[JPT][hapmap]
rs1079008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12447201	0.95[ASN][1000 genomes]
rs12597529	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12599669	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12925954	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12926007	0.81[ASN][1000 genomes]
rs12935145	0.99[ASN][1000 genomes]
rs1520229	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs1520230	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs1520232	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs1520234	1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs1520236	0.86[JPT][hapmap]
rs1520241	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1520243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1532418	0.86[JPT][hapmap]
rs16942779	0.81[ASN][1000 genomes]
rs16968098	0.81[ASN][1000 genomes]
rs16968101	0.81[ASN][1000 genomes]
rs16968102	0.81[ASN][1000 genomes]
rs16968480	0.93[JPT][hapmap]
rs1850966	0.97[ASN][1000 genomes]
rs185394	0.85[ASN][1000 genomes]
rs1874457	0.99[ASN][1000 genomes]
rs1874458	0.99[ASN][1000 genomes]
rs1874459	0.99[ASN][1000 genomes]
rs1879260	0.99[ASN][1000 genomes]
rs1896755	0.81[ASN][1000 genomes]
rs1896756	0.81[ASN][1000 genomes]
rs1908723	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915117	0.86[JPT][hapmap]
rs2088285	0.93[JPT][hapmap]
rs2280396	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs257335	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs257336	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs257337	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs257341	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs257487	0.97[ASN][1000 genomes]
rs257490	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs257497	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs257498	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs257499	0.83[ASN][1000 genomes]
rs28216	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs34699531	0.81[ASN][1000 genomes]
rs34893901	0.81[ASN][1000 genomes]
rs35139	0.88[ASN][1000 genomes]
rs35140	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs35144	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs35145	0.87[ASN][1000 genomes]
rs35146	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs35148	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs35149	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs35150	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs35152	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs35154	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs35155	0.85[ASN][1000 genomes]
rs35156	0.85[ASN][1000 genomes]
rs35157	0.84[ASN][1000 genomes]
rs35158	0.84[ASN][1000 genomes]
rs35159	0.84[ASN][1000 genomes]
rs35160	0.84[ASN][1000 genomes]
rs35161	0.84[ASN][1000 genomes]
rs35162	0.84[ASN][1000 genomes]
rs35163	0.85[ASN][1000 genomes]
rs35164	0.85[ASN][1000 genomes]
rs35165	0.82[ASN][1000 genomes]
rs35166	0.85[ASN][1000 genomes]
rs35167	0.85[ASN][1000 genomes]
rs35169	0.85[ASN][1000 genomes]
rs35170	0.85[ASN][1000 genomes]
rs35171	0.85[ASN][1000 genomes]
rs35176	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs35177	0.96[ASN][1000 genomes]
rs35178	0.94[ASN][1000 genomes]
rs35179	0.94[ASN][1000 genomes]
rs35180	0.93[ASN][1000 genomes]
rs35188	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs35191	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs35192	0.94[CHB][hapmap];0.93[ASN][1000 genomes]
rs35193	0.91[ASN][1000 genomes]
rs35195	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs35198	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs35199	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs35200	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs35203	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs35204	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs35205	0.93[ASN][1000 genomes]
rs35206	0.93[ASN][1000 genomes]
rs35208	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs35209	1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs35210	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs35214	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs35215	0.93[ASN][1000 genomes]
rs35216	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs35218	0.93[ASN][1000 genomes]
rs35219	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs35224	0.91[ASN][1000 genomes]
rs35226	0.91[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs35263777	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35557609	0.81[ASN][1000 genomes]
rs35891857	0.81[ASN][1000 genomes]
rs369499	0.85[ASN][1000 genomes]
rs382418	0.85[ASN][1000 genomes]
rs385317	0.81[ASN][1000 genomes]
rs388039	0.85[ASN][1000 genomes]
rs396950	0.85[ASN][1000 genomes]
rs400182	0.85[ASN][1000 genomes]
rs40113	0.85[ASN][1000 genomes]
rs40115	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs40116	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs40510	0.85[ASN][1000 genomes]
rs406925	0.85[ASN][1000 genomes]
rs408330	0.81[ASN][1000 genomes]
rs422274	0.85[ASN][1000 genomes]
rs42863	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs436962	0.81[ASN][1000 genomes]
rs437402	0.85[ASN][1000 genomes]
rs437408	0.85[ASN][1000 genomes]
rs447096	0.85[ASN][1000 genomes]
rs462735	0.89[ASN][1000 genomes]
rs4967858	0.81[ASN][1000 genomes]
rs4967859	0.81[ASN][1000 genomes]
rs4967860	0.81[ASN][1000 genomes]
rs4967861	0.81[ASN][1000 genomes]
rs4967862	0.81[ASN][1000 genomes]
rs4967866	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4967868	0.91[JPT][hapmap]
rs4967875	0.81[ASN][1000 genomes]
rs4967876	0.81[ASN][1000 genomes]
rs4967882	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs4967886	0.93[JPT][hapmap]
rs59954387	0.97[ASN][1000 genomes]
rs610896	0.81[ASN][1000 genomes]
rs611241	0.81[ASN][1000 genomes]
rs611322	0.81[ASN][1000 genomes]
rs62042237	0.97[ASN][1000 genomes]
rs7204729	1.00[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7498801	0.93[JPT][hapmap]
rs765771	0.84[CEU][hapmap]
rs8048351	0.92[EUR][1000 genomes]
rs8048383	0.81[ASN][1000 genomes]
rs878359	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs909003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs973200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs974782	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs990639	0.97[ASN][1000 genomes]
rs9935608	1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.94[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	nsv948640	chr16:64859061-65112790	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv833260	chr16:65050647-65218759	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1831	chr16:65071976-65106105	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1520231	CMTM1	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:65039000-65089600	Weak transcription	Fetal Intestine Large	intestine
2	chr16:65039600-65079800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr16:65040600-65086000	Weak transcription	HMEC	breast
4	chr16:65047200-65078400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr16:65058600-65104400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr16:65059800-65078400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr16:65066800-65076800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr16:65066800-65078400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr16:65069800-65105000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr16:65071800-65077400	Weak transcription	NHLF	lung
11	chr16:65072600-65077800	Weak transcription	Brain Germinal Matrix	brain
12	chr16:65072800-65077200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr16:65072800-65078000	Weak transcription	Fetal Brain Female	brain
14	chr16:65072800-65078400	Weak transcription	Fetal Brain Male	brain
15	chr16:65072800-65088800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr16:65072800-65096200	Weak transcription	Colon Smooth Muscle	Colon
17	chr16:65073000-65078600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr16:65074400-65077600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr16:65074400-65084800	Strong transcription	Fetal Lung	lung
20	chr16:65074400-65094000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr16:65074600-65076800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr16:65074600-65077800	Strong transcription	Osteobl	bone
23	chr16:65074800-65077200	Strong transcription	NHDF-Ad	bronchial
24	chr16:65074800-65077800	Strong transcription	NH-A	brain
25	chr16:65074800-65078200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr16:65075000-65077000	Strong transcription	Fetal Stomach	stomach
27	chr16:65075000-65082200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr16:65075200-65077400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr16:65075200-65077400	Strong transcription	Stomach Smooth Muscle	stomach
30	chr16:65075200-65077600	Strong transcription	HSMM	muscle
31	chr16:65075200-65077800	Strong transcription	HSMMtube	muscle
32	chr16:65075200-65078000	Weak transcription	Fetal Kidney	kidney
33	chr16:65075600-65080400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr16:65075800-65078600	Weak transcription	Aorta	Aorta
35	chr16:65076000-65079200	Enhancers	Brain Hippocampus Middle	brain
36	chr16:65076200-65076800	Weak transcription	Brain Anterior Caudate	brain
37	chr16:65076200-65077400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr16:65076200-65077800	Genic enhancers	Fetal Muscle Leg	muscle
39	chr16:65076200-65079000	Enhancers	Brain Angular Gyrus	brain
40	chr16:65076400-65076800	Weak transcription	Spleen	Spleen
41	chr16:65076400-65077400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr16:65076400-65078800	Strong transcription	Ovary	ovary
43	chr16:65076400-65079000	Enhancers	Brain Cingulate Gyrus	brain
44	chr16:65076400-65079600	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr16:65076600-65077000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr16:65076600-65079800	Enhancers	Brain Substantia Nigra	brain
47	chr16:65076600-65081200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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