Variant report

Variant	rs579750
Chromosome Location	chr3:138280668-138280669
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10804658	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1082034	0.83[EUR][1000 genomes]
rs1082037	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1088055	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10935287	0.83[EUR][1000 genomes]
rs11717771	0.83[EUR][1000 genomes]
rs12487652	0.83[EUR][1000 genomes]
rs12487694	0.84[EUR][1000 genomes]
rs12490633	0.83[EUR][1000 genomes]
rs12497070	0.83[EUR][1000 genomes]
rs12636910	0.83[EUR][1000 genomes]
rs13101081	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1379257	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1479930	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1600511	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1672927	0.80[EUR][1000 genomes]
rs1672932	0.84[EUR][1000 genomes]
rs1672938	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1672939	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1672963	0.85[EUR][1000 genomes]
rs1673593	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1673594	0.85[EUR][1000 genomes]
rs1673607	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1673608	0.84[EUR][1000 genomes]
rs1673612	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1673622	0.83[EUR][1000 genomes]
rs1673624	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2124868	0.84[AMR][1000 genomes]
rs2348146	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2607790	0.84[EUR][1000 genomes]
rs2607795	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2881793	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs361073	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs361074	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs361075	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs361076	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs361077	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4432674	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4678264	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs484698	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4894389	0.84[EUR][1000 genomes]
rs497334	0.84[EUR][1000 genomes]
rs503922	0.83[EUR][1000 genomes]
rs529615	0.83[EUR][1000 genomes]
rs542010	0.80[EUR][1000 genomes]
rs550507	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs559313	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs564800	0.81[EUR][1000 genomes]
rs586946	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs587005	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs587331	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60513493	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs609497	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs609797	0.80[EUR][1000 genomes]
rs611134	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61699523	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs618792	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs620035	0.83[EUR][1000 genomes]
rs629884	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs634374	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs642258	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6439810	0.80[EUR][1000 genomes]
rs664928	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6771237	0.80[EUR][1000 genomes]
rs6798058	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs680070	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7625326	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7627685	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7634745	0.86[EUR][1000 genomes]
rs7643973	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7653815	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs773444	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs773445	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs773448	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs773449	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs773450	0.83[EUR][1000 genomes]
rs773452	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs773456	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs811322	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs811793	0.83[EUR][1000 genomes]
rs814022	0.81[EUR][1000 genomes]
rs936316	0.83[EUR][1000 genomes]
rs9811052	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9817419	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9827256	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9848718	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9853998	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9878436	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv522517	chr3:138174523-138297982	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv877538	chr3:138218709-138311201	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	esv3429877	chr3:138272946-138325019	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
12	esv3448925	chr3:138277303-138312046	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs579750	FAIM	Cis_1M	lymphoblastoid	RTeQTL
rs579750	CEP70	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138255800-138282000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:138262000-138281800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:138267600-138292000	Weak transcription	Fetal Heart	heart
4	chr3:138268600-138291200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:138268600-138297800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:138268800-138282800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:138268800-138287400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:138268800-138293000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:138269000-138306800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:138274600-138281800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:138275200-138291800	Weak transcription	Fetal Kidney	kidney
12	chr3:138278400-138281400	ZNF genes & repeats	Brain Germinal Matrix	brain
13	chr3:138278400-138292800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:138278800-138296200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:138279000-138288000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:138279000-138296800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:138279000-138298400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:138279200-138281600	Weak transcription	Gastric	stomach
19	chr3:138279200-138292400	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:138279400-138292000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:138279400-138292800	Weak transcription	Left Ventricle	heart
22	chr3:138279600-138280800	Strong transcription	Ovary	ovary
23	chr3:138279600-138281200	Weak transcription	HepG2	liver
24	chr3:138279600-138289000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:138279600-138290400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:138279600-138291200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:138279600-138292800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:138279600-138297800	Weak transcription	Right Ventricle	heart
29	chr3:138279600-138300400	Weak transcription	Colonic Mucosa	Colon
30	chr3:138279800-138281200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:138279800-138291800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:138279800-138296400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:138280000-138282200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:138280000-138282800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:138280000-138285200	Weak transcription	Thymus	Thymus
36	chr3:138280000-138285600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:138280000-138286000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:138280000-138286200	Weak transcription	Dnd41	blood
39	chr3:138280000-138286800	Weak transcription	Fetal Stomach	stomach
40	chr3:138280000-138288000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:138280000-138288600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:138280000-138288600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr3:138280000-138288600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:138280000-138291200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:138280000-138291400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:138280000-138291800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:138280000-138292000	Weak transcription	Adipose Nuclei	Adipose
48	chr3:138280000-138292000	Weak transcription	Fetal Lung	lung
49	chr3:138280000-138292600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:138280000-138292800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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