Variant report

Variant	rs811793
Chromosome Location	chr3:138210855-138210856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10804658	0.81[AMR][1000 genomes]
rs1082037	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1088055	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10935284	1.00[ASN][1000 genomes]
rs13098789	0.81[EUR][1000 genomes]
rs13101081	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1379257	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1479930	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1600511	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1672938	0.85[EUR][1000 genomes]
rs1672939	0.83[EUR][1000 genomes]
rs1673593	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1673607	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1673612	0.81[AMR][1000 genomes]
rs1673624	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1679167	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679168	1.00[ASN][1000 genomes]
rs1679175	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1720836	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347469	1.00[ASN][1000 genomes]
rs2348146	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2607795	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2881793	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35471402	0.83[EUR][1000 genomes]
rs361073	0.82[AMR][1000 genomes]
rs361074	0.81[AMR][1000 genomes]
rs361075	0.81[AMR][1000 genomes]
rs361076	0.81[AMR][1000 genomes]
rs361077	0.81[AMR][1000 genomes]
rs3884240	0.83[EUR][1000 genomes]
rs4432674	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4678264	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678265	1.00[ASN][1000 genomes]
rs4678266	0.88[EUR][1000 genomes]
rs4678420	1.00[ASN][1000 genomes]
rs484698	0.82[AMR][1000 genomes]
rs550507	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs559313	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs579750	0.83[EUR][1000 genomes]
rs586946	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs587005	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs587331	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60513493	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs609497	0.82[AMR][1000 genomes]
rs611134	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61699523	0.81[AMR][1000 genomes]
rs618792	0.85[EUR][1000 genomes]
rs629884	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs634374	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6439809	0.84[EUR][1000 genomes]
rs664928	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6762114	0.83[EUR][1000 genomes]
rs6798058	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs680070	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73229526	0.81[EUR][1000 genomes]
rs7625326	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626226	0.84[EUR][1000 genomes]
rs7627685	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7634745	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643973	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7645920	0.82[EUR][1000 genomes]
rs7653815	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773444	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs773445	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs773448	0.81[EUR][1000 genomes]
rs773449	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs773452	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs773456	0.82[AMR][1000 genomes]
rs774003	0.90[ASN][1000 genomes]
rs774004	0.93[ASN][1000 genomes]
rs774005	0.97[ASN][1000 genomes]
rs774006	0.97[ASN][1000 genomes]
rs774007	0.97[ASN][1000 genomes]
rs774008	0.97[ASN][1000 genomes]
rs808925	0.97[ASN][1000 genomes]
rs811792	0.97[ASN][1000 genomes]
rs9811052	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817419	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9822037	0.83[EUR][1000 genomes]
rs9827256	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9848718	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853998	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878436	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9879213	0.90[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
rs811793	FAIM	Cis_1M	lymphoblastoid	RTeQTL
rs811793	CEP70	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 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	chr3:138204800-138211000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:138205000-138211600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:138207000-138223800	Weak transcription	Brain Anterior Caudate	brain
7	chr3:138207600-138211800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:138208200-138211000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:138208200-138211400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:138208400-138211800	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:138208400-138212200	Weak transcription	HSMM	muscle
12	chr3:138208400-138227400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:138208600-138211200	Weak transcription	Fetal Thymus	thymus
14	chr3:138208600-138215000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:138208800-138211200	Weak transcription	Liver	Liver
16	chr3:138208800-138211200	Weak transcription	Fetal Intestine Small	intestine
17	chr3:138208800-138213400	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:138209000-138211000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:138209000-138211600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:138209200-138218400	Weak transcription	Gastric	stomach
21	chr3:138209400-138211800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:138209400-138212600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:138209400-138236800	Weak transcription	Aorta	Aorta
24	chr3:138209600-138211600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:138209600-138212800	Weak transcription	HSMMtube	muscle
26	chr3:138209800-138211000	Weak transcription	Dnd41	blood
27	chr3:138209800-138211600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:138209800-138212200	Weak transcription	NHLF	lung
29	chr3:138209800-138258600	Weak transcription	Primary T cells from cord blood	blood
30	chr3:138210000-138211400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:138210000-138212000	Weak transcription	Ovary	ovary
32	chr3:138210000-138218400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:138210000-138230200	Weak transcription	Fetal Brain Male	brain
34	chr3:138210200-138211600	Weak transcription	Fetal Brain Female	brain
35	chr3:138210200-138215000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:138210200-138222000	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:138210400-138211000	Weak transcription	Fetal Lung	lung
38	chr3:138210400-138211200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:138210400-138215200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:138210400-138218400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:138210400-138236800	Weak transcription	Brain Substantia Nigra	brain
42	chr3:138210400-138242000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:138210800-138211000	ZNF genes & repeats	Fetal Stomach	stomach
44	chr3:138210800-138211000	Enhancers	Right Ventricle	heart
45	chr3:138210800-138211200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
46	chr3:138210800-138211200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:138210800-138211600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:138210800-138211600	Enhancers	Right Atrium	heart
49	chr3:138210800-138211600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:138210800-138212400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links