Variant report

Variant	rs11078374
Chromosome Location	chr17:17036743-17036744
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10852847	1.00[CHB][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078376	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11656868	1.00[CHB][hapmap]
rs11867506	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11871902	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1974721	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2090018	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2271520	1.00[CHB][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2349646	1.00[ASN][1000 genomes]
rs28461224	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4247118	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4247120	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4275914	1.00[ASN][1000 genomes]
rs4514740	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4985696	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985701	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4985702	1.00[CHB][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4985717	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985740	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4985746	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4985778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6502563	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7206981	1.00[ASN][1000 genomes]
rs7207485	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7208929	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7208973	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7217091	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7220827	1.00[CHB][hapmap]
rs7221842	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7222311	1.00[ASN][1000 genomes]
rs8064550	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8072184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073842	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8079563	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9893911	1.00[ASN][1000 genomes]
rs9898995	1.00[ASN][1000 genomes]
rs9908767	1.00[ASN][1000 genomes]
rs9914671	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907728	chr17:17013189-17095487	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv984510	chr17:17015688-17048858	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv524958	chr17:17029718-17060805	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11078374	TOM1L2	cis	cerebellum	SCAN
rs11078374	TRPV2	cis	parietal	SCAN
rs11078374	FLCN	cis	cerebellum	SCAN
rs11078374	FLCN	cis	parietal	SCAN
rs11078374	ULK2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17024200-17043200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr17:17024400-17039800	Weak transcription	Small Intestine	intestine
3	chr17:17024600-17045600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr17:17027400-17042400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr17:17027400-17043000	Strong transcription	NHEK	skin
6	chr17:17027400-17043400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr17:17028000-17038200	Genic enhancers	Fetal Muscle Trunk	muscle
8	chr17:17029800-17043400	Strong transcription	NHLF	lung
9	chr17:17029800-17044200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr17:17029800-17088400	Strong transcription	Dnd41	blood
11	chr17:17030000-17041800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr17:17030000-17042800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr17:17030000-17042800	Strong transcription	A549	lung
14	chr17:17030000-17043200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr17:17030000-17043200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr17:17030000-17043600	Strong transcription	Esophagus	oesophagus
17	chr17:17030000-17048200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr17:17030000-17052200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr17:17030000-17088000	Strong transcription	Duodenum Mucosa	Duodenum
20	chr17:17030200-17037000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:17030200-17037400	Strong transcription	Colon Smooth Muscle	Colon
22	chr17:17030200-17037400	Strong transcription	Rectal Smooth Muscle	rectum
23	chr17:17030200-17037800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr17:17030200-17042800	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr17:17030200-17043800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr17:17030200-17051600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr17:17030200-17055000	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr17:17030400-17038800	Genic enhancers	Brain Hippocampus Middle	brain
29	chr17:17030400-17043800	Strong transcription	Adipose Nuclei	Adipose
30	chr17:17030400-17044800	Strong transcription	Primary B cells from cord blood	blood
31	chr17:17030400-17047600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr17:17030400-17047800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr17:17030400-17055800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr17:17030400-17059800	Strong transcription	Fetal Intestine Small	intestine
35	chr17:17030400-17079200	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr17:17030400-17089200	Strong transcription	Fetal Intestine Large	intestine
37	chr17:17030600-17040600	Genic enhancers	Brain Anterior Caudate	brain
38	chr17:17030600-17042800	Strong transcription	Osteobl	bone
39	chr17:17030600-17045000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr17:17030600-17051000	Strong transcription	Colonic Mucosa	Colon
41	chr17:17030800-17038800	Genic enhancers	Brain Angular Gyrus	brain
42	chr17:17030800-17042800	Strong transcription	Thymus	Thymus
43	chr17:17030800-17043400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:17031000-17040000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr17:17031000-17043600	Strong transcription	HSMM	muscle
46	chr17:17031000-17078800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr17:17031200-17038000	Strong transcription	Fetal Brain Female	brain
48	chr17:17031200-17057200	Strong transcription	Primary T cells from cord blood	blood
49	chr17:17031200-17067800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr17:17031400-17037000	Strong transcription	Stomach Mucosa	stomach

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