Variant report

Variant	rs1322787
Chromosome Location	chr13:50010199-50010200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11619265	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs12050042	0.80[ASW][hapmap]
rs12429813	0.92[CEU][hapmap]
rs1358991	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543513	0.95[CEU][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1980795	0.86[ASW][hapmap]
rs2038638	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs2057414	0.92[CEU][hapmap]
rs2077848	0.96[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs2407691	0.83[ASN][1000 genomes]
rs4340215	0.80[MEX][hapmap]
rs4941643	0.88[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs4942830	0.93[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4942833	0.80[MEX][hapmap]
rs61959992	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs721457	0.96[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7317772	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7327520	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7987940	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7991226	0.85[ASN][1000 genomes]
rs7995283	0.96[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs7997737	0.92[CEU][hapmap]
rs9316454	0.92[CEU][hapmap]
rs9526563	0.81[ASN][1000 genomes]
rs9535244	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535247	0.95[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv430558	chr13:49914393-50059354	Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430559	chr13:49930369-50059354	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430560	chr13:49930643-50059354	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv430562	chr13:49930643-50067246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv430564	chr13:49945247-50059354	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv430566	chr13:49945247-50089844	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv430571	chr13:49961137-50059354	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv430570	chr13:49961137-50089844	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv1807924	chr13:49991885-50036730	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv1796315	chr13:49992988-50031868	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv523648	chr13:50005444-50086266	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1322787	CAB39L	Cis_1M	lymphoblastoid	RTeQTL
rs1322787	CAB39L	cis	cerebellum	SCAN
rs1322787	RCBTB1	cis	cerebellum	SCAN
rs1322787	PHF11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49975800-50013600	Weak transcription	Primary B cells from cord blood	blood
2	chr13:49978400-50016800	Weak transcription	Fetal Brain Male	brain
3	chr13:49983400-50017000	Weak transcription	Brain Anterior Caudate	brain
4	chr13:49983400-50017400	Weak transcription	Lung	lung
5	chr13:49983600-50017000	Weak transcription	Brain Angular Gyrus	brain
6	chr13:49984400-50010200	Weak transcription	Brain Substantia Nigra	brain
7	chr13:49993800-50017400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr13:49994000-50016200	Weak transcription	NHLF	lung
9	chr13:49994000-50017000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr13:49994000-50017200	Weak transcription	HSMM	muscle
11	chr13:49994200-50010200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr13:49994200-50017200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr13:49994600-50016000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:49994800-50017200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr13:49995400-50017000	Weak transcription	Liver	Liver
16	chr13:49995600-50017000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr13:49995800-50017000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr13:49996400-50010200	Weak transcription	Brain Hippocampus Middle	brain
19	chr13:49997000-50017000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr13:49997000-50017200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr13:49997400-50017200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr13:49998600-50017000	Weak transcription	Adipose Nuclei	Adipose
23	chr13:49999000-50017400	Weak transcription	Small Intestine	intestine
24	chr13:50000000-50013400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr13:50000200-50010800	Weak transcription	Colon Smooth Muscle	Colon
26	chr13:50000200-50017200	Weak transcription	Fetal Intestine Small	intestine
27	chr13:50000400-50017000	Weak transcription	Fetal Lung	lung
28	chr13:50000600-50011000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr13:50000600-50017400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr13:50002600-50017000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr13:50002600-50017000	Weak transcription	HSMMtube	muscle
32	chr13:50002800-50017000	Weak transcription	Primary T cells from cord blood	blood
33	chr13:50002800-50017000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr13:50002800-50017200	Weak transcription	Fetal Muscle Leg	muscle
35	chr13:50003000-50017000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr13:50003000-50017200	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr13:50003400-50010200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr13:50003400-50017000	Weak transcription	Brain Germinal Matrix	brain
39	chr13:50003400-50017200	Weak transcription	Fetal Stomach	stomach
40	chr13:50003400-50017200	Weak transcription	Ovary	ovary
41	chr13:50005200-50017000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr13:50005200-50017200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr13:50006600-50010200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr13:50006600-50016200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr13:50006800-50016200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr13:50006800-50017000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr13:50007200-50017200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr13:50007200-50017200	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr13:50007400-50017000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr13:50007400-50017200	Weak transcription	Primary T cells fromperipheralblood	blood

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