Variant report

Variant	rs1555672
Chromosome Location	chr13:49901088-49901089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11619804	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs11838927	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11843587	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12585196	0.96[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1924659	0.92[CEU][hapmap];0.91[GIH][hapmap]
rs1924660	0.92[CEU][hapmap]
rs2147398	0.92[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2181905	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2274149	0.92[CEU][hapmap]
rs2274150	0.92[CEU][hapmap];0.90[GIH][hapmap]
rs2407521	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2407608	0.92[CEU][hapmap]
rs2407609	0.92[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3751418	0.87[JPT][hapmap]
rs3764131	0.92[CEU][hapmap];0.85[GIH][hapmap]
rs4245351	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4941637	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4942812	0.92[CEU][hapmap];0.91[GIH][hapmap]
rs4942815	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6561511	0.91[CEU][hapmap]
rs719614	0.92[CEU][hapmap]
rs7326181	0.85[EUR][1000 genomes]
rs7326191	0.92[CEU][hapmap];0.91[GIH][hapmap]
rs7328063	0.85[EUR][1000 genomes]
rs7330892	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7336018	0.83[ASW][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap]
rs7984689	0.92[CEU][hapmap]
rs7985932	0.85[GIH][hapmap]
rs7992766	0.85[GIH][hapmap]
rs7997545	0.92[CEU][hapmap];0.91[GIH][hapmap]
rs9316434	0.92[CEU][hapmap];0.91[GIH][hapmap]
rs9316439	0.91[CEU][hapmap];0.87[CHB][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9526532	0.81[CHD][hapmap]
rs9526533	0.91[CEU][hapmap]
rs9526534	0.92[CEU][hapmap]
rs9535174	0.91[CEU][hapmap]
rs9535179	0.83[JPT][hapmap]
rs9535181	0.92[CEU][hapmap];0.91[GIH][hapmap]
rs9535184	0.92[CEU][hapmap];0.91[GIH][hapmap]
rs9535193	0.91[CEU][hapmap];0.94[GIH][hapmap];0.81[EUR][1000 genomes]
rs9535194	0.82[EUR][1000 genomes]
rs9535197	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535198	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535199	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535200	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568177	0.92[CEU][hapmap];0.91[GIH][hapmap]
rs9568181	0.81[EUR][1000 genomes]
rs9568182	0.84[EUR][1000 genomes]
rs9591249	0.92[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9596077	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9596078	0.81[EUR][1000 genomes]
rs9596079	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596080	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9596082	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv832607	chr13:49756458-49920894	Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900069	chr13:49815405-49976393	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1555672	CAB39L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49876200-49935600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr13:49881800-49906800	Weak transcription	Fetal Brain Male	brain
3	chr13:49884600-49933600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr13:49884800-49903800	Weak transcription	Fetal Brain Female	brain
5	chr13:49884800-49914200	Weak transcription	Brain Hippocampus Middle	brain
6	chr13:49884800-49925600	Weak transcription	Brain Substantia Nigra	brain
7	chr13:49885600-49933400	Weak transcription	Primary T cells from cord blood	blood
8	chr13:49885800-49926000	Weak transcription	Brain Germinal Matrix	brain
9	chr13:49888400-49903800	Weak transcription	Right Ventricle	heart
10	chr13:49888400-49904000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr13:49888400-49922200	Weak transcription	Gastric	stomach
12	chr13:49888600-49905600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:49888600-49922200	Weak transcription	Lung	lung
14	chr13:49888800-49903600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr13:49888800-49905400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:49888800-49908800	Weak transcription	Fetal Intestine Large	intestine
17	chr13:49889000-49944600	Weak transcription	Brain Angular Gyrus	brain
18	chr13:49889000-49947600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr13:49889200-49919400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr13:49889200-49933400	Weak transcription	Brain Anterior Caudate	brain
21	chr13:49889200-49944600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr13:49889600-49914200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr13:49889600-49914400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr13:49889600-49914400	Weak transcription	Small Intestine	intestine
25	chr13:49889600-49927400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr13:49891800-49922000	Weak transcription	Left Ventricle	heart
27	chr13:49894400-49905200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr13:49894600-49910400	Weak transcription	Adipose Nuclei	Adipose
29	chr13:49894800-49904000	Weak transcription	HSMMtube	muscle
30	chr13:49895000-49916400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr13:49895000-49927600	Weak transcription	NHLF	lung
32	chr13:49895200-49910800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr13:49895200-49914200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr13:49895600-49918000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr13:49895600-49933200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr13:49895800-49901600	Weak transcription	Ovary	ovary
37	chr13:49895800-49935600	Weak transcription	Esophagus	oesophagus
38	chr13:49897600-49904000	Weak transcription	Aorta	Aorta
39	chr13:49897600-49905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr13:49897800-49906000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr13:49897800-49916800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr13:49898200-49902000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr13:49898200-49904000	Weak transcription	Fetal Stomach	stomach
44	chr13:49899200-49906400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr13:49900600-49901200	Weak transcription	Psoas Muscle	Psoas
46	chr13:49900600-49902000	Enhancers	Liver	Liver
47	chr13:49900600-49903800	Weak transcription	Fetal Heart	heart
48	chr13:49900600-49904000	Weak transcription	Pancreas	Pancrea
49	chr13:49900600-49904200	Weak transcription	Right Atrium	heart
50	chr13:49900800-49903800	Weak transcription	Colon Smooth Muscle	Colon

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