Variant report

Variant	rs3993323
Chromosome Location	chr11:17954082-17954083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12290125	1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17720417	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17720513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17721739	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs17794213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17794760	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs211126	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs211127	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs211134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs211138	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2237912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2237921	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2237924	0.87[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2237931	1.00[YRI][hapmap]
rs2237933	1.00[YRI][hapmap]
rs2237934	1.00[YRI][hapmap]
rs2283236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34614478	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs394218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3993324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs440234	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4438010	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4756927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757604	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4757605	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4757606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757615	0.90[CEU][hapmap]
rs61882454	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61882456	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61882460	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61882461	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61884488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884489	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884492	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61884493	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61884494	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7114572	1.00[YRI][hapmap]
rs758437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931469	1.00[YRI][hapmap]
rs7940992	1.00[YRI][hapmap]

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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv832079	chr11:17927967-18047743	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3993323	HPS5	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17838400-17971600	Weak transcription	Gastric	stomach
2	chr11:17886000-17965200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr11:17896000-17968000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr11:17896400-17968000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:17906000-17970200	Weak transcription	Lung	lung
6	chr11:17914600-17965400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr11:17915800-17966000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr11:17920600-17976000	Weak transcription	Esophagus	oesophagus
9	chr11:17928600-17970200	Weak transcription	Thymus	Thymus
10	chr11:17929200-17954800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr11:17933000-17956800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:17934400-18033600	Weak transcription	Small Intestine	intestine
13	chr11:17935200-17955000	Strong transcription	Primary T cells from cord blood	blood
14	chr11:17937600-17977000	Weak transcription	Colon Smooth Muscle	Colon
15	chr11:17937800-17965800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr11:17940000-17976400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr11:17942800-17954400	Weak transcription	NHEK	skin
18	chr11:17943600-17975400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:17943800-17992800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr11:17944000-17964600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:17944000-17975600	Weak transcription	HSMM	muscle
22	chr11:17944000-18026600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:17944200-17955400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:17945000-17965400	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr11:17945000-17974000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:17945200-17954200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr11:17945200-17967600	Weak transcription	Adipose Nuclei	Adipose
28	chr11:17945200-17974800	Weak transcription	GM12878-XiMat	blood
29	chr11:17945400-17960400	Weak transcription	Dnd41	blood
30	chr11:17945400-17961800	Weak transcription	Brain Angular Gyrus	brain
31	chr11:17945400-17962200	Weak transcription	Ovary	ovary
32	chr11:17945400-17975400	Weak transcription	Pancreas	Pancrea
33	chr11:17945400-18010000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:17945400-18033400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:17945600-17961000	Weak transcription	Right Ventricle	heart
36	chr11:17945600-17969600	Weak transcription	Fetal Brain Female	brain
37	chr11:17945600-17972400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr11:17946200-17975400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:17948000-17970200	Weak transcription	Spleen	Spleen
40	chr11:17948600-17967600	Weak transcription	Aorta	Aorta
41	chr11:17948600-17967800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:17948800-17981400	Weak transcription	Fetal Brain Male	brain
43	chr11:17949200-17967600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr11:17949400-17969800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr11:17949600-17972600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr11:17949600-17974200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:17949800-17965400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr11:17949800-17968400	Weak transcription	Brain Hippocampus Middle	brain
49	chr11:17950000-17954200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:17950000-17954200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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