Variant report

Variant	rs9864693
Chromosome Location	chr3:51656370-51656371
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11709482	0.80[AMR][1000 genomes]
rs11719995	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11917683	1.00[CEU][hapmap]
rs11919197	0.85[CEU][hapmap]
rs13090011	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.83[MEX][hapmap];0.99[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3821829	0.85[CEU][hapmap]
rs4067	0.85[CEU][hapmap]
rs4234644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4355273	0.85[CEU][hapmap]
rs4468965	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4494918	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687721	1.00[CEU][hapmap]
rs4687770	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap]
rs4687771	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6775666	0.85[CEU][hapmap]
rs6787312	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9841077	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9864443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9866430	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv997264	chr3:51584056-51689648	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536570	chr3:51584056-51689648	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv999553	chr3:51584056-51696052	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9864693	HEMK1	cis	cerebellum	SCAN
rs9864693	TEX264	cis	Nerve Tibial	GTEx
rs9864693	IQCF2	cis	parietal	SCAN
rs9864693	TEX264	cis	Esophagus Muscularis	GTEx
rs9864693	TEX264	cis	Artery Tibial	GTEx
rs9864693	MST1	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51625400-51663400	Weak transcription	Right Ventricle	heart
2	chr3:51625600-51658200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:51626000-51656600	Weak transcription	Placenta	Placenta
4	chr3:51628800-51660800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:51630400-51661400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:51630800-51661400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:51631000-51661400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:51631000-51661600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:51631000-51661600	Weak transcription	Fetal Thymus	thymus
10	chr3:51631800-51660800	Weak transcription	Primary B cells from cord blood	blood
11	chr3:51636200-51661200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:51637600-51660800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:51640200-51656400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:51640600-51661000	Weak transcription	Dnd41	blood
15	chr3:51640600-51661200	Weak transcription	Thymus	Thymus
16	chr3:51640600-51663200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:51643000-51660800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:51643600-51656600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:51643800-51661000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:51643800-51661000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:51648800-51656400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:51649800-51663400	Weak transcription	GM12878-XiMat	blood
23	chr3:51650400-51657600	Enhancers	Liver	Liver
24	chr3:51651800-51656800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:51652400-51656600	Enhancers	HepG2	liver
26	chr3:51652600-51657600	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr3:51652600-51661000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:51652800-51657600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:51653400-51657400	Enhancers	Stomach Smooth Muscle	stomach
30	chr3:51653600-51656600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr3:51653600-51657600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:51653600-51657600	Enhancers	Colon Smooth Muscle	Colon
33	chr3:51653600-51657600	Enhancers	Rectal Smooth Muscle	rectum
34	chr3:51653800-51657200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:51653800-51657200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:51653800-51657600	Enhancers	NHLF	lung
37	chr3:51654000-51656600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:51654000-51657000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:51654000-51657000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:51654000-51657000	Enhancers	Osteobl	bone
41	chr3:51654000-51657200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr3:51654200-51656400	Weak transcription	Brain Anterior Caudate	brain
43	chr3:51654200-51656600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr3:51654200-51657000	Enhancers	NHEK	skin
45	chr3:51654200-51661200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:51654600-51656800	Enhancers	Stomach Mucosa	stomach
47	chr3:51654600-51656800	Enhancers	HMEC	breast
48	chr3:51654600-51657000	Enhancers	HSMM	muscle
49	chr3:51654600-51657400	Enhancers	HSMMtube	muscle
50	chr3:51654600-51657600	Enhancers	Skeletal Muscle Female	skeletal muscle

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