Variant report

Variant	rs9535206
Chromosome Location	chr13:49932011-49932012
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10467382	1.00[CEU][hapmap];1.00[CHB][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]
rs11148144	1.00[CHB][hapmap]
rs12323239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994157	1.00[ASN][1000 genomes]
rs9316440	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316441	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316444	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9316445	1.00[CHB][hapmap]
rs9526544	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9526545	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526547	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9526548	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535214	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596087	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9535206	SETDB2	cis	cerebellum	SCAN
rs9535206	CAB39L	cis	cerebellum	SCAN

Chromatin state (count:62 , 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	chr13:49884600-49933600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr13:49885600-49933400	Weak transcription	Primary T cells from cord blood	blood
4	chr13:49889000-49944600	Weak transcription	Brain Angular Gyrus	brain
5	chr13:49889000-49947600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr13:49889200-49933400	Weak transcription	Brain Anterior Caudate	brain
7	chr13:49889200-49944600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr13:49895600-49933200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr13:49895800-49935600	Weak transcription	Esophagus	oesophagus
10	chr13:49912600-49948800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr13:49913200-49932600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr13:49915000-49941400	Weak transcription	Brain Hippocampus Middle	brain
13	chr13:49922200-49937600	Weak transcription	Fetal Brain Male	brain
14	chr13:49922200-49937600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr13:49922400-49940800	Weak transcription	Lung	lung
16	chr13:49922400-49946600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr13:49922400-49947800	Weak transcription	Right Ventricle	heart
18	chr13:49922800-49951400	Weak transcription	Gastric	stomach
19	chr13:49923000-49935000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr13:49923200-49934800	Weak transcription	Fetal Stomach	stomach
21	chr13:49923200-49935000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr13:49923200-49937800	Weak transcription	Primary B cells from cord blood	blood
23	chr13:49923200-49951200	Weak transcription	Pancreas	Pancrea
24	chr13:49926000-49933200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr13:49926400-49934400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr13:49926400-49937600	Weak transcription	Brain Substantia Nigra	brain
27	chr13:49926800-49937800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr13:49928600-49932400	Enhancers	NHDF-Ad	bronchial
29	chr13:49929000-49936000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr13:49929400-49933400	Weak transcription	Fetal Heart	heart
31	chr13:49929400-49950000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr13:49929600-49934800	Weak transcription	Brain Germinal Matrix	brain
33	chr13:49929600-49936400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr13:49929800-49933000	Weak transcription	Fetal Brain Female	brain
35	chr13:49929800-49935200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr13:49929800-49937000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr13:49929800-49937600	Weak transcription	Liver	Liver
38	chr13:49930000-49932200	Enhancers	Rectal Smooth Muscle	rectum
39	chr13:49930000-49932200	Enhancers	HSMMtube	muscle
40	chr13:49930000-49932400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr13:49930000-49932400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr13:49930000-49932400	Enhancers	NHLF	lung
43	chr13:49930000-49932400	Enhancers	Osteobl	bone
44	chr13:49930000-49932800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr13:49930200-49932200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr13:49930200-49932400	Enhancers	NH-A	brain
47	chr13:49930600-49932400	Enhancers	HSMM	muscle
48	chr13:49930800-49932200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr13:49930800-49932200	Enhancers	Aorta	Aorta
50	chr13:49930800-49932200	Enhancers	Colon Smooth Muscle	Colon

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