Variant report

Variant	rs3766686
Chromosome Location	chr1:175155978-175155979
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:175154624..175159314-chr1:175159716..175163217,5	K562	blood:

Variant related genes	Relation type
ENSG00000235750	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1008459	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136973	0.86[ASW][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs2205604	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2272785	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861158	0.86[ASW][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs3753559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753560	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766690	0.86[ASW][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap]
rs3766691	0.81[CHB][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap]
rs3766695	0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949473	chr1:175151666-175391741	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3766686	FMO1	cis	cerebellum	SCAN
rs3766686	KIAA0040	cis	Artery Tibial	GTEx
rs3766686	SNORD79	cis	parietal	SCAN
rs3766686	KIAA0040	cis	lymphoblastoid	seeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175129200-175159600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:175135000-175158400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:175136000-175157600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:175141000-175160200	Weak transcription	HUVEC	blood vessel
5	chr1:175141400-175158400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:175143000-175160800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:175143600-175158000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:175146000-175157800	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr1:175146200-175159400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:175146200-175159800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:175146800-175160400	Weak transcription	Fetal Intestine Large	intestine
12	chr1:175147000-175156200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:175147600-175160400	Weak transcription	Colonic Mucosa	Colon
14	chr1:175148200-175157400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr1:175148200-175157600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr1:175148200-175157800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:175148400-175159200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:175148800-175158000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:175151400-175157400	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr1:175151400-175157400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr1:175152200-175156000	Strong transcription	NHEK	skin
22	chr1:175152200-175159600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:175152400-175157200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:175153000-175156400	Weak transcription	Fetal Stomach	stomach
25	chr1:175153600-175156000	Enhancers	Primary T cells from cord blood	blood
26	chr1:175153600-175156400	Enhancers	Adipose Nuclei	Adipose
27	chr1:175153600-175159600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:175153800-175156000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:175153800-175156000	Weak transcription	Gastric	stomach
30	chr1:175153800-175157200	Weak transcription	Fetal Thymus	thymus
31	chr1:175153800-175157600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:175153800-175158000	Weak transcription	Esophagus	oesophagus
33	chr1:175153800-175160400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:175154600-175156200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:175154600-175158400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:175154800-175156200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:175154800-175156400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr1:175155000-175156000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:175155200-175156800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
40	chr1:175155200-175157200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:175155400-175156600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr1:175155400-175156600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr1:175155600-175156000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr1:175155600-175156000	Enhancers	Liver	Liver
45	chr1:175155600-175156000	Enhancers	Left Ventricle	heart
46	chr1:175155600-175156200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:175155600-175156200	Genic enhancers	Fetal Muscle Leg	muscle
48	chr1:175155600-175156400	Enhancers	Lung	lung
49	chr1:175155600-175156600	Enhancers	Primary hematopoietic stem cells	blood
50	chr1:175155600-175156600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood

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