Variant report

Variant	rs6817242
Chromosome Location	chr4:88307986-88307987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11097148	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11722370	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11727469	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11945520	1.00[CHB][hapmap]
rs4305486	1.00[CHB][hapmap]
rs4435709	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4585263	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635784	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55721398	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55806847	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56156416	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56354112	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56878407	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57124432	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61376571	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62319098	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62319099	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62319100	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62319101	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62319102	0.90[EUR][1000 genomes]
rs62319103	0.90[EUR][1000 genomes]
rs62319104	0.90[EUR][1000 genomes]
rs62319105	0.90[EUR][1000 genomes]
rs62319109	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62319110	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531974	1.00[CHB][hapmap]
rs6531985	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66699153	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67026749	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6811010	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]
rs6817185	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818142	0.90[EUR][1000 genomes]
rs6833678	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834947	1.00[CHB][hapmap]
rs6839488	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839620	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840102	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840247	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6846149	1.00[CHB][hapmap]
rs6849382	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6849846	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6850337	1.00[CHB][hapmap]
rs7661455	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662471	1.00[CHB][hapmap]
rs7664479	1.00[CHB][hapmap]
rs7668285	1.00[CHB][hapmap]
rs7676494	1.00[CHB][hapmap]
rs7677036	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682516	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682892	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697960	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9684766	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9684778	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

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	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6817242	HSD17B13	cis	cerebellar cortex	BrainEAC
rs6817242	HSD17B13	cis	brain	BrainEAC
rs6817242	HSD17B13	cis	intralobular white matter	BrainEAC

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88254800-88311800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:88256200-88310600	Weak transcription	Right Ventricle	heart
3	chr4:88257800-88311800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:88267400-88308000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr4:88276200-88311400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:88287400-88308000	Weak transcription	Spleen	Spleen
7	chr4:88291000-88309000	Weak transcription	Right Atrium	heart
8	chr4:88293000-88308000	Weak transcription	Colonic Mucosa	Colon
9	chr4:88293000-88308800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:88293000-88309600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:88293000-88311200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:88293200-88308000	Weak transcription	Left Ventricle	heart
13	chr4:88293200-88309600	Weak transcription	Brain Hippocampus Middle	brain
14	chr4:88293200-88309600	Weak transcription	Gastric	stomach
15	chr4:88293200-88311400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:88293400-88308000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr4:88293400-88309800	Weak transcription	Brain Anterior Caudate	brain
18	chr4:88294000-88309400	Weak transcription	NHLF	lung
19	chr4:88294000-88309600	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:88294000-88311000	Weak transcription	HSMM	muscle
21	chr4:88294200-88310800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr4:88294600-88308000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:88294800-88308000	Weak transcription	Lung	lung
24	chr4:88294800-88309400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:88295000-88308000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:88295200-88309400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:88295400-88311200	Weak transcription	Aorta	Aorta
28	chr4:88296000-88308000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:88296200-88309000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:88297000-88308200	Weak transcription	Hela-S3	cervix
31	chr4:88297400-88308200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:88297400-88309400	Weak transcription	Brain Substantia Nigra	brain
33	chr4:88297400-88309600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:88297400-88309600	Weak transcription	A549	lung
35	chr4:88297400-88310000	Weak transcription	NHDF-Ad	bronchial
36	chr4:88297400-88310600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:88297400-88310800	Weak transcription	Osteobl	bone
38	chr4:88302800-88312000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:88303200-88309200	Weak transcription	Primary T cells from cord blood	blood
40	chr4:88303200-88309400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:88303200-88309400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:88303400-88308400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr4:88303400-88309000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:88303400-88309400	Weak transcription	Thymus	Thymus
45	chr4:88303600-88308000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr4:88303600-88308400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr4:88303600-88309400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:88303600-88310400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr4:88303600-88310400	Weak transcription	Placenta	Placenta
50	chr4:88303800-88309400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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