Variant report

Variant	rs4967866
Chromosome Location	chr16:65002591-65002592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDH5-20	chr16:65001684-65003539	ucscGeneNc_uc002eoo_1

Extended variants
information (count: 159 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs1025311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1040270	0.86[JPT][hapmap]
rs1079008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12445593	0.87[ASN][1000 genomes]
rs12447201	0.90[ASN][1000 genomes]
rs12597529	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12925954	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12926007	0.89[ASN][1000 genomes]
rs12935145	0.90[ASN][1000 genomes]
rs1402020	0.84[LWK][hapmap];0.81[YRI][hapmap]
rs1520229	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1520230	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs1520231	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]
rs1520232	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs1520234	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs1520236	0.86[JPT][hapmap]
rs1520241	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1532418	0.86[JPT][hapmap]
rs16942779	0.88[ASN][1000 genomes]
rs16968098	0.88[ASN][1000 genomes]
rs16968101	0.88[ASN][1000 genomes]
rs16968102	0.88[ASN][1000 genomes]
rs16968480	0.80[JPT][hapmap]
rs1850966	0.91[ASN][1000 genomes]
rs185394	0.92[ASN][1000 genomes]
rs1874457	0.90[ASN][1000 genomes]
rs1874458	0.90[ASN][1000 genomes]
rs1874459	0.90[ASN][1000 genomes]
rs1879260	0.90[ASN][1000 genomes]
rs1896755	0.88[ASN][1000 genomes]
rs1896756	0.88[ASN][1000 genomes]
rs1908723	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1915117	0.86[JPT][hapmap]
rs2088285	0.80[JPT][hapmap]
rs2115393	0.84[ASN][1000 genomes]
rs2280396	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs257335	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs257336	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs257337	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs257340	0.81[YRI][hapmap]
rs257341	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs257487	0.91[ASN][1000 genomes]
rs257490	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs257497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs257498	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs257499	0.90[ASN][1000 genomes]
rs28216	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs34699531	0.88[ASN][1000 genomes]
rs34893901	0.88[ASN][1000 genomes]
rs35139	0.95[ASN][1000 genomes]
rs35140	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs35144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs35145	0.94[ASN][1000 genomes]
rs35146	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs35148	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs35149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35155	0.92[ASN][1000 genomes]
rs35156	0.92[ASN][1000 genomes]
rs35157	0.91[ASN][1000 genomes]
rs35158	0.91[ASN][1000 genomes]
rs35159	0.91[ASN][1000 genomes]
rs35160	0.91[ASN][1000 genomes]
rs35161	0.91[ASN][1000 genomes]
rs35162	0.91[ASN][1000 genomes]
rs35163	0.92[ASN][1000 genomes]
rs35164	0.92[ASN][1000 genomes]
rs35165	0.90[ASN][1000 genomes]
rs35166	0.92[ASN][1000 genomes]
rs35167	0.92[ASN][1000 genomes]
rs35169	0.92[ASN][1000 genomes]
rs35170	0.92[ASN][1000 genomes]
rs35171	0.92[ASN][1000 genomes]
rs35176	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs35177	0.90[ASN][1000 genomes]
rs35178	0.94[ASN][1000 genomes]
rs35179	0.94[ASN][1000 genomes]
rs35180	0.95[ASN][1000 genomes]
rs35188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs35191	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs35192	0.94[CHB][hapmap];0.95[ASN][1000 genomes]
rs35193	0.93[ASN][1000 genomes]
rs35195	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs35198	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs35199	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs35200	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs35201	0.82[YRI][hapmap]
rs35203	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs35204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs35205	0.95[ASN][1000 genomes]
rs35206	0.95[ASN][1000 genomes]
rs35208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs35209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs35210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35213	0.82[YRI][hapmap]
rs35214	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs35215	0.95[ASN][1000 genomes]
rs35216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs35218	0.95[ASN][1000 genomes]
rs35219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs35224	0.97[ASN][1000 genomes]
rs35226	0.91[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs35229	0.85[YRI][hapmap]
rs35230	0.82[YRI][hapmap]
rs35232	0.80[YRI][hapmap]
rs35263777	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35557609	0.88[ASN][1000 genomes]
rs35891857	0.88[ASN][1000 genomes]
rs369499	0.92[ASN][1000 genomes]
rs382418	0.92[ASN][1000 genomes]
rs385317	0.88[ASN][1000 genomes]
rs388039	0.92[ASN][1000 genomes]
rs396950	0.92[ASN][1000 genomes]
rs400182	0.92[ASN][1000 genomes]
rs40113	0.92[ASN][1000 genomes]
rs40115	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs40116	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs40510	0.92[ASN][1000 genomes]
rs406925	0.92[ASN][1000 genomes]
rs408330	0.88[ASN][1000 genomes]
rs422274	0.92[ASN][1000 genomes]
rs42863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs436962	0.89[ASN][1000 genomes]
rs437402	0.92[ASN][1000 genomes]
rs437408	0.92[ASN][1000 genomes]
rs447096	0.92[ASN][1000 genomes]
rs453866	0.87[ASN][1000 genomes]
rs462735	0.96[ASN][1000 genomes]
rs4967858	0.88[ASN][1000 genomes]
rs4967859	0.88[ASN][1000 genomes]
rs4967860	0.88[ASN][1000 genomes]
rs4967861	0.88[ASN][1000 genomes]
rs4967862	0.88[ASN][1000 genomes]
rs4967875	0.88[ASN][1000 genomes]
rs4967876	0.88[ASN][1000 genomes]
rs4967882	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs4967886	0.80[JPT][hapmap]
rs59954387	0.88[ASN][1000 genomes]
rs610896	0.88[ASN][1000 genomes]
rs611241	0.88[ASN][1000 genomes]
rs611322	0.88[ASN][1000 genomes]
rs62042237	0.91[ASN][1000 genomes]
rs7188339	0.86[ASN][1000 genomes]
rs7189660	0.86[ASN][1000 genomes]
rs7204729	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7498801	0.80[JPT][hapmap]
rs765771	0.84[CEU][hapmap]
rs8048351	0.83[EUR][1000 genomes]
rs8048383	0.89[ASN][1000 genomes]
rs878359	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs909003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs973200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs974782	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs990639	0.91[ASN][1000 genomes]
rs9935608	1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4967866	CMTM1	cis	cerebellum	SCAN
rs4967866	SUPT4H1	trans	cerebellum	SCAN
rs4967866	FAM96B	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:64980000-65005200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr16:64983000-65003200	Weak transcription	Brain Substantia Nigra	brain
3	chr16:64983200-65004400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr16:64984800-65004600	Weak transcription	Fetal Brain Female	brain
5	chr16:64984800-65005400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr16:64985000-65004400	Weak transcription	Fetal Intestine Large	intestine
7	chr16:64985000-65005200	Weak transcription	Brain Germinal Matrix	brain
8	chr16:64985000-65005800	Weak transcription	Aorta	Aorta
9	chr16:64985000-65011000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr16:64985200-65004400	Weak transcription	Fetal Brain Male	brain
11	chr16:64985400-65004200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr16:64985400-65004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr16:64985400-65005800	Weak transcription	Spleen	Spleen
14	chr16:64985400-65015200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr16:64986200-65003000	Weak transcription	Brain Hippocampus Middle	brain
16	chr16:64986200-65004200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr16:64986400-65004000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr16:64986400-65004200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr16:64987000-65002600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr16:64987000-65003200	Weak transcription	NHLF	lung
21	chr16:64991200-65004200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr16:64991400-65032600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr16:64995000-65004400	Weak transcription	Fetal Muscle Leg	muscle
24	chr16:64998000-65024800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr16:64998200-65002600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr16:64998400-65004400	Weak transcription	HMEC	breast
27	chr16:64998400-65014800	Weak transcription	HUVEC	blood vessel
28	chr16:64998800-65002600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr16:64999200-65010200	Strong transcription	HSMM	muscle
30	chr16:64999200-65017800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr16:64999200-65017800	Strong transcription	NH-A	brain
32	chr16:64999600-65003800	Weak transcription	Ovary	ovary
33	chr16:64999600-65005000	Weak transcription	Fetal Kidney	kidney
34	chr16:65000000-65005000	Weak transcription	Placenta	Placenta
35	chr16:65000600-65002800	Strong transcription	NHDF-Ad	bronchial
36	chr16:65000800-65051000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr16:65001200-65006800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr16:65001200-65007000	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr16:65001200-65012600	Strong transcription	Fetal Lung	lung
40	chr16:65001400-65002600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr16:65002000-65002600	Strong transcription	Fetal Stomach	stomach
42	chr16:65002200-65003200	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr16:65002200-65003800	Enhancers	Brain Anterior Caudate	brain
44	chr16:65002200-65003800	Enhancers	HSMMtube	muscle
45	chr16:65002200-65004200	Genic enhancers	Osteobl	bone
46	chr16:65002200-65005400	Enhancers	Fetal Heart	heart
47	chr16:65002400-65002600	Enhancers	Brain Angular Gyrus	brain
48	chr16:65002400-65002800	Active TSS	Brain Cingulate Gyrus	brain
49	chr16:65002400-65003200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr16:65002400-65004000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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