Variant report

Variant	rs9366950
Chromosome Location	chr6:38216694-38216695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38210095..38212639-chr6:38215015..38217311,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10484932	0.97[ASN][1000 genomes]
rs12055689	0.96[ASN][1000 genomes]
rs12055699	0.97[ASN][1000 genomes]
rs12176364	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.93[ASN][1000 genomes]
rs16890428	1.00[YRI][hapmap]
rs60235041	0.85[ASN][1000 genomes]
rs7356828	0.97[ASN][1000 genomes]
rs7356829	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7356904	0.97[ASN][1000 genomes]
rs7745176	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7755820	0.80[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7756174	0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7756345	0.87[ASN][1000 genomes]
rs7756480	0.87[ASN][1000 genomes]
rs915161	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs926564	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9296234	1.00[YRI][hapmap]
rs9296239	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9296240	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9296241	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9296242	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9349056	1.00[YRI][hapmap]
rs9349060	0.97[ASN][1000 genomes]
rs9349061	0.80[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9349062	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9349063	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9349077	1.00[YRI][hapmap]
rs9357262	1.00[YRI][hapmap]
rs9357265	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9357266	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9357267	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9366949	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9369040	0.93[ASN][1000 genomes]
rs9369041	0.97[ASN][1000 genomes]
rs9369057	1.00[YRI][hapmap]
rs9380717	1.00[YRI][hapmap]
rs9380726	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9394481	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9394482	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9462415	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9470832	0.97[ASN][1000 genomes]
rs9470834	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9470835	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9366950	PRICKLE4	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38178000-38221600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:38178000-38221800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:38181400-38229400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:38194400-38230200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:38204800-38229400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:38205200-38228800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:38207800-38229400	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:38208000-38221600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:38208000-38222400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:38208000-38226400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:38208200-38222200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:38208200-38226000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:38208200-38227600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:38208200-38236600	Weak transcription	Gastric	stomach
15	chr6:38208200-38255000	Weak transcription	Ovary	ovary
16	chr6:38208600-38222400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr6:38209000-38229000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:38209200-38227000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:38209600-38221000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:38210800-38221000	Weak transcription	Primary B cells from cord blood	blood
21	chr6:38210800-38221200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:38211800-38221600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:38212000-38221600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:38213000-38220800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:38213000-38222000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr6:38213200-38222800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr6:38213200-38223000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:38213400-38221600	Weak transcription	Esophagus	oesophagus
29	chr6:38213400-38221800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:38213400-38228800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:38213400-38232400	Weak transcription	Right Ventricle	heart
32	chr6:38215000-38222400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr6:38215200-38217400	Enhancers	Aorta	Aorta
34	chr6:38215200-38222800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr6:38215200-38229400	Weak transcription	Brain Angular Gyrus	brain
36	chr6:38215600-38217600	Weak transcription	Fetal Lung	lung
37	chr6:38215600-38221600	Weak transcription	Left Ventricle	heart
38	chr6:38215600-38229000	Weak transcription	Brain Substantia Nigra	brain
39	chr6:38216000-38216800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr6:38216000-38229000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr6:38216000-38238000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr6:38216200-38216800	Enhancers	HMEC	breast
43	chr6:38216400-38216800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:38216400-38216800	Enhancers	NHEK	skin
45	chr6:38216400-38217200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:38216400-38221200	Weak transcription	Primary T cells from cord blood	blood
47	chr6:38216600-38216800	Enhancers	Hela-S3	cervix
48	chr6:38216600-38220600	Weak transcription	Lung	lung
49	chr6:38216600-38221200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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