Variant report

Variant	rs1672963
Chromosome Location	chr3:138274551-138274552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1082034	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082037	0.86[EUR][1000 genomes]
rs1088055	0.83[EUR][1000 genomes]
rs10935287	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11717771	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487652	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12487694	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490633	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12497070	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12632793	0.80[ASN][1000 genomes]
rs12632794	0.80[ASN][1000 genomes]
rs12636246	0.81[ASN][1000 genomes]
rs12636910	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13067864	0.80[ASN][1000 genomes]
rs13069355	0.80[ASN][1000 genomes]
rs13073978	0.80[ASN][1000 genomes]
rs13084780	0.80[ASN][1000 genomes]
rs13093668	0.80[ASN][1000 genomes]
rs13098789	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1379257	0.88[EUR][1000 genomes]
rs1625751	0.92[ASN][1000 genomes]
rs1672927	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1672928	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1672931	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1672932	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1672933	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1672936	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1672938	0.85[EUR][1000 genomes]
rs1672939	0.83[EUR][1000 genomes]
rs1673593	0.88[EUR][1000 genomes]
rs1673594	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673607	0.87[EUR][1000 genomes]
rs1673608	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1673622	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1673624	0.86[EUR][1000 genomes]
rs1679165	0.80[ASN][1000 genomes]
rs1679169	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1720833	0.92[ASN][1000 genomes]
rs2086351	0.92[ASN][1000 genomes]
rs2348146	0.86[EUR][1000 genomes]
rs2607790	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607795	0.86[EUR][1000 genomes]
rs28719641	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2881793	0.81[EUR][1000 genomes]
rs34011134	0.80[ASN][1000 genomes]
rs34284415	0.80[ASN][1000 genomes]
rs34316974	0.80[ASN][1000 genomes]
rs35034861	0.80[ASN][1000 genomes]
rs35471402	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35500947	0.94[ASN][1000 genomes]
rs35932955	0.92[ASN][1000 genomes]
rs3884240	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4432674	0.88[EUR][1000 genomes]
rs4678266	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4894389	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs497334	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs503922	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs529615	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs537210	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs542010	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550507	0.84[EUR][1000 genomes]
rs559313	0.86[EUR][1000 genomes]
rs56394118	0.94[ASN][1000 genomes]
rs564800	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579750	0.85[EUR][1000 genomes]
rs582386	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586946	0.86[EUR][1000 genomes]
rs587005	0.86[EUR][1000 genomes]
rs587331	0.86[EUR][1000 genomes]
rs59371015	0.80[ASN][1000 genomes]
rs609497	0.82[EUR][1000 genomes]
rs609797	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs611134	0.83[EUR][1000 genomes]
rs612471	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs618792	0.85[EUR][1000 genomes]
rs620035	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629884	0.83[EUR][1000 genomes]
rs634374	0.85[EUR][1000 genomes]
rs6439809	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6439810	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs654528	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs656107	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs664928	0.86[EUR][1000 genomes]
rs6762114	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6771237	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6798058	0.86[EUR][1000 genomes]
rs680070	0.88[EUR][1000 genomes]
rs73229526	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7626226	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7643973	0.83[EUR][1000 genomes]
rs7645920	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs773443	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs773444	0.85[EUR][1000 genomes]
rs773445	0.85[EUR][1000 genomes]
rs773448	0.81[EUR][1000 genomes]
rs773449	0.83[EUR][1000 genomes]
rs773450	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs773452	0.84[EUR][1000 genomes]
rs773455	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs774011	0.92[ASN][1000 genomes]
rs774012	0.92[ASN][1000 genomes]
rs814022	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936316	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9681127	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9817419	0.83[EUR][1000 genomes]
rs9822037	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9823182	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9855306	0.92[ASN][1000 genomes]
rs9880928	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1672963	FAIM	cis	Muscle Skeletal	GTEx
rs1672963	FAIM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138239800-138277200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:138255800-138282000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:138262000-138281800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:138267600-138276000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:138267600-138292000	Weak transcription	Fetal Heart	heart
6	chr3:138268200-138278400	Weak transcription	Brain Anterior Caudate	brain
7	chr3:138268400-138278200	Weak transcription	Aorta	Aorta
8	chr3:138268600-138278200	Weak transcription	Esophagus	oesophagus
9	chr3:138268600-138278200	Weak transcription	Pancreas	Pancrea
10	chr3:138268600-138279000	Weak transcription	Colonic Mucosa	Colon
11	chr3:138268600-138291200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:138268600-138297800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:138268800-138274800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:138268800-138278200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:138268800-138278200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:138268800-138278200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:138268800-138278400	Weak transcription	Left Ventricle	heart
18	chr3:138268800-138278800	Weak transcription	Right Ventricle	heart
19	chr3:138268800-138278800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:138268800-138279000	Weak transcription	Gastric	stomach
21	chr3:138268800-138279200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:138268800-138282800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:138268800-138287400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:138268800-138293000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:138269000-138274600	Weak transcription	Dnd41	blood
26	chr3:138269000-138278800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:138269000-138278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:138269000-138279200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:138269000-138306800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:138269200-138274800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:138269400-138278200	Weak transcription	Liver	Liver
32	chr3:138269600-138279400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:138270200-138278400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:138271000-138274600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:138271400-138278800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:138271600-138277800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:138271800-138278600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:138272800-138279400	Weak transcription	Primary T cells from cord blood	blood
39	chr3:138273000-138274600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:138273000-138275000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
41	chr3:138273000-138275200	ZNF genes & repeats	Fetal Lung	lung
42	chr3:138273400-138278000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:138273600-138275000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
44	chr3:138273600-138275200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:138273600-138275600	Strong transcription	Fetal Thymus	thymus
46	chr3:138274000-138274800	Weak transcription	Thymus	Thymus
47	chr3:138274000-138275000	Weak transcription	Lung	lung
48	chr3:138274000-138278000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr3:138274000-138278200	Weak transcription	Ovary	ovary
50	chr3:138274200-138275000	Weak transcription	Fetal Stomach	stomach

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