Variant report

Variant	rs9535416
Chromosome Location	chr13:50624140-50624141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11839292	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12876820	1.00[JPT][hapmap]
rs1323450	1.00[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1622458	0.85[EUR][1000 genomes]
rs2066544	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2066557	0.83[YRI][hapmap]
rs2066581	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2066593	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2066600	0.86[EUR][1000 genomes]
rs2407884	0.86[AFR][1000 genomes]
rs2740509	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2760911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6561570	0.85[AFR][1000 genomes]
rs706610	0.82[CEU][hapmap]
rs7318151	1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9316482	0.92[CEU][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9316484	1.00[JPT][hapmap]
rs9526629	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9535407	0.83[YRI][hapmap]
rs9535410	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9535411	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9535414	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568354	0.83[YRI][hapmap]
rs9740075	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription 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	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv1054415	chr13:50598121-50650938	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1202 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9535416	C13orf1	cis	cerebellum	SCAN
rs9535416	DLEU1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50578600-50629800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr13:50578800-50654400	Weak transcription	Esophagus	oesophagus
3	chr13:50586800-50654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:50587000-50633800	Weak transcription	Hela-S3	cervix
5	chr13:50587000-50645600	Weak transcription	Spleen	Spleen
6	chr13:50588000-50645600	Weak transcription	Ovary	ovary
7	chr13:50589800-50645600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr13:50590000-50624200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr13:50590200-50653600	Weak transcription	Small Intestine	intestine
10	chr13:50594600-50635000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr13:50594800-50641000	Weak transcription	Lung	lung
12	chr13:50594800-50643200	Weak transcription	Brain Hippocampus Middle	brain
13	chr13:50594800-50643600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr13:50595000-50654200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr13:50595200-50640000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr13:50595800-50654400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr13:50597000-50624600	Weak transcription	Fetal Lung	lung
18	chr13:50598200-50629800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr13:50598200-50634800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr13:50598200-50641000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr13:50598600-50626000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr13:50598600-50627800	Weak transcription	Brain Germinal Matrix	brain
23	chr13:50598600-50640000	Weak transcription	Placenta	Placenta
24	chr13:50598600-50650200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr13:50601600-50626200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr13:50601600-50641000	Weak transcription	Left Ventricle	heart
27	chr13:50604800-50634000	Weak transcription	NHEK	skin
28	chr13:50608600-50639800	Weak transcription	NHLF	lung
29	chr13:50611800-50646400	Strong transcription	Fetal Thymus	thymus
30	chr13:50612200-50639800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr13:50612400-50639800	Strong transcription	Dnd41	blood
32	chr13:50612400-50643000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr13:50612600-50639800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr13:50612600-50644200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr13:50612800-50645400	Weak transcription	HSMMtube	muscle
36	chr13:50614000-50643800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr13:50615200-50643200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr13:50615600-50624800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr13:50616000-50653600	Weak transcription	Fetal Kidney	kidney
40	chr13:50616600-50639800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr13:50617400-50625600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr13:50617400-50625800	Weak transcription	Primary B cells from cord blood	blood
43	chr13:50617400-50626000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr13:50617400-50626000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr13:50617400-50626400	Weak transcription	Fetal Intestine Large	intestine
46	chr13:50617400-50634200	Weak transcription	Adipose Nuclei	Adipose
47	chr13:50617400-50640400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr13:50617400-50650000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr13:50617400-50654200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr13:50617600-50626000	Weak transcription	Primary T cells from cord blood	blood

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