Variant report

Variant	rs4678266
Chromosome Location	chr3:138211521-138211522
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1082034	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10935281	0.80[EUR][1000 genomes]
rs10935282	0.81[ASN][1000 genomes]
rs10935287	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11709290	0.87[ASN][1000 genomes]
rs11717771	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12487652	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12487694	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12490633	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12497070	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12636910	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13098789	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13101081	0.83[EUR][1000 genomes]
rs1479930	0.88[EUR][1000 genomes]
rs1600511	0.88[EUR][1000 genomes]
rs1625751	0.99[ASN][1000 genomes]
rs1672927	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1672928	0.83[AMR][1000 genomes]
rs1672931	0.83[AMR][1000 genomes]
rs1672932	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1672933	0.83[AMR][1000 genomes]
rs1672936	0.82[AMR][1000 genomes]
rs1672963	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1673594	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1673608	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1673622	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1679165	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1679169	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1720833	0.99[ASN][1000 genomes]
rs2086351	0.99[ASN][1000 genomes]
rs2607790	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28719641	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2881793	0.81[EUR][1000 genomes]
rs35471402	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35500947	0.90[ASN][1000 genomes]
rs35932955	0.84[ASN][1000 genomes]
rs3813264	0.88[ASN][1000 genomes]
rs3884240	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4678264	0.88[EUR][1000 genomes]
rs4678418	0.81[AMR][1000 genomes]
rs4894389	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs497334	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs503922	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs529615	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs537210	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs542010	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56236670	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56394118	0.89[ASN][1000 genomes]
rs564800	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs582386	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs609797	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs612471	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs620035	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6439809	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439810	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs654528	0.83[AMR][1000 genomes]
rs656107	0.83[ASN][1000 genomes]
rs66644444	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67037472	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6762114	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6763380	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6771237	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73229526	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7625326	0.83[EUR][1000 genomes]
rs7626226	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7627685	0.85[EUR][1000 genomes]
rs7634745	0.85[EUR][1000 genomes]
rs7645920	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7653815	0.85[EUR][1000 genomes]
rs773443	0.85[ASN][1000 genomes]
rs773450	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs773455	0.84[AMR][1000 genomes]
rs774011	0.99[ASN][1000 genomes]
rs774012	0.99[ASN][1000 genomes]
rs811793	0.88[EUR][1000 genomes]
rs814022	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs936316	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9681127	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9811052	0.83[EUR][1000 genomes]
rs9822037	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9823182	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9827256	0.83[EUR][1000 genomes]
rs9848718	0.83[EUR][1000 genomes]
rs9848938	0.87[ASN][1000 genomes]
rs9853998	0.81[EUR][1000 genomes]
rs9855306	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	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
3	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4678266	FAIM	cis	Muscle Skeletal	GTEx
rs4678266	FAIM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138188000-138211600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:138194000-138260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:138199400-138211600	Weak transcription	Fetal Heart	heart
4	chr3:138205000-138211600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:138207000-138223800	Weak transcription	Brain Anterior Caudate	brain
6	chr3:138207600-138211800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:138208400-138211800	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:138208400-138212200	Weak transcription	HSMM	muscle
9	chr3:138208400-138227400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:138208600-138215000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:138208800-138213400	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:138209000-138211600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:138209200-138218400	Weak transcription	Gastric	stomach
14	chr3:138209400-138211800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:138209400-138212600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:138209400-138236800	Weak transcription	Aorta	Aorta
17	chr3:138209600-138211600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:138209600-138212800	Weak transcription	HSMMtube	muscle
19	chr3:138209800-138211600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:138209800-138212200	Weak transcription	NHLF	lung
21	chr3:138209800-138258600	Weak transcription	Primary T cells from cord blood	blood
22	chr3:138210000-138212000	Weak transcription	Ovary	ovary
23	chr3:138210000-138218400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:138210000-138230200	Weak transcription	Fetal Brain Male	brain
25	chr3:138210200-138211600	Weak transcription	Fetal Brain Female	brain
26	chr3:138210200-138215000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:138210200-138222000	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:138210400-138215200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:138210400-138218400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:138210400-138236800	Weak transcription	Brain Substantia Nigra	brain
31	chr3:138210400-138242000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:138210800-138211600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:138210800-138211600	Enhancers	Right Atrium	heart
34	chr3:138210800-138211600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:138210800-138212400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:138210800-138212400	ZNF genes & repeats	Pancreas	Pancrea
37	chr3:138210800-138212400	ZNF genes & repeats	Thymus	Thymus
38	chr3:138210800-138212600	ZNF genes & repeats	Lung	lung
39	chr3:138210800-138212600	Enhancers	Psoas Muscle	Psoas
40	chr3:138210800-138213200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr3:138210800-138213200	Strong transcription	Stomach Smooth Muscle	stomach
42	chr3:138210800-138214400	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:138210800-138260600	Weak transcription	Colonic Mucosa	Colon
44	chr3:138211000-138211600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:138211000-138211600	Weak transcription	Esophagus	oesophagus
46	chr3:138211000-138211800	Weak transcription	Right Ventricle	heart
47	chr3:138211000-138212400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:138211000-138212600	Strong transcription	Fetal Stomach	stomach
49	chr3:138211000-138213000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr3:138211000-138213400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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