Variant report

Variant	rs1393957
Chromosome Location	chr11:19172911-19172912
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10741761	0.83[TSI][hapmap]
rs10833064	0.82[TSI][hapmap]
rs11604483	0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs11606057	0.85[JPT][hapmap]
rs12801321	0.87[GIH][hapmap];0.86[JPT][hapmap]
rs1546327	0.81[JPT][hapmap]
rs1546329	0.88[EUR][1000 genomes]
rs1863383	0.86[EUR][1000 genomes]
rs2042687	0.81[JPT][hapmap]
rs2042688	0.82[TSI][hapmap]
rs2271001	0.81[TSI][hapmap]
rs3802798	0.86[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs4757758	0.83[TSI][hapmap]
rs7129212	0.83[TSI][hapmap]
rs905552	0.82[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040805	chr11:19037871-19892803	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv540957	chr11:19037871-19892803	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1393957	NAV2	cis	cerebellum	SCAN
rs1393957	SAA2	cis	cerebellum	SCAN
rs1393957	SLC6A12	trans	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:19139600-19175000	Weak transcription	Pancreas	Pancrea
2	chr11:19140000-19186400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:19140200-19175000	Weak transcription	Thymus	Thymus
4	chr11:19140800-19186800	Weak transcription	Colonic Mucosa	Colon
5	chr11:19142800-19173200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr11:19143400-19185800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr11:19143400-19186400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:19143400-19201600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:19143600-19197400	Weak transcription	Small Intestine	intestine
10	chr11:19147600-19174200	Weak transcription	Osteobl	bone
11	chr11:19152800-19175000	Weak transcription	Psoas Muscle	Psoas
12	chr11:19153200-19186600	Weak transcription	Aorta	Aorta
13	chr11:19154000-19175000	Weak transcription	Ovary	ovary
14	chr11:19154400-19174800	Weak transcription	Left Ventricle	heart
15	chr11:19154800-19177200	Weak transcription	NHEK	skin
16	chr11:19156400-19175400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:19156600-19193200	Weak transcription	Fetal Stomach	stomach
18	chr11:19156800-19193800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:19156800-19194200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:19157200-19186200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:19161600-19194400	Weak transcription	HSMM	muscle
22	chr11:19162200-19176200	Weak transcription	Gastric	stomach
23	chr11:19162800-19203000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr11:19163400-19178000	Weak transcription	Fetal Brain Female	brain
25	chr11:19164000-19200400	Weak transcription	Fetal Brain Male	brain
26	chr11:19164600-19177600	Weak transcription	Fetal Lung	lung
27	chr11:19164800-19175200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr11:19166200-19186200	Weak transcription	Brain Anterior Caudate	brain
29	chr11:19166400-19203000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr11:19166800-19186400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:19167000-19194200	Weak transcription	Fetal Kidney	kidney
32	chr11:19167200-19173000	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr11:19167400-19176600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:19167400-19184800	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr11:19167400-19186600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:19167400-19194200	Weak transcription	Brain Hippocampus Middle	brain
37	chr11:19167600-19184200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr11:19167800-19176600	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr11:19167800-19177000	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr11:19167800-19181600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr11:19167800-19181800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr11:19167800-19199400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr11:19168000-19175000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:19168000-19201600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr11:19168400-19175000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr11:19168400-19176600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr11:19168400-19181400	Strong transcription	Dnd41	blood
48	chr11:19168400-19182200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:19168400-19184400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr11:19168800-19174600	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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