Variant report

Variant	rs3790450
Chromosome Location	chr1:93091065-93091066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs11164803	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs11164814	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs11164816	0.88[AMR][1000 genomes]
rs11164820	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11577426	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs11578004	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11578098	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11581176	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11581705	0.88[AMR][1000 genomes]
rs11583778	0.84[AMR][1000 genomes]
rs11585590	0.88[AMR][1000 genomes]
rs11588509	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11588545	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589122	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11589660	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11591094	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11800409	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs11800771	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11800848	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11801763	0.88[YRI][hapmap]
rs11803097	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs11804321	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11805007	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805229	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11805698	0.86[AMR][1000 genomes]
rs11807962	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809055	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11810217	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs12730641	0.82[AFR][1000 genomes]
rs12731107	0.81[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12733238	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738833	0.94[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12743005	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12743520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12746893	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs12749480	0.83[EUR][1000 genomes]
rs12749786	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs12756698	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12756786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333743	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051841	0.84[EUR][1000 genomes]
rs2893226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34202284	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs34221961	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34231012	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34250288	0.88[AMR][1000 genomes]
rs34305407	0.83[EUR][1000 genomes]
rs34734076	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34761380	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34812295	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34843292	0.85[AMR][1000 genomes]
rs35038369	0.88[AMR][1000 genomes]
rs35241270	0.91[AMR][1000 genomes]
rs35311203	0.83[EUR][1000 genomes]
rs35435370	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35526187	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35612297	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35699160	0.83[AMR][1000 genomes]
rs35705463	0.86[AMR][1000 genomes]
rs35901796	0.82[AMR][1000 genomes]
rs36114576	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41286801	0.85[ASN][1000 genomes]
rs41313373	0.85[ASN][1000 genomes]
rs4642892	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56044027	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56307974	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56406332	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59864761	0.84[AMR][1000 genomes]
rs6660889	0.85[ASN][1000 genomes]
rs6689470	0.85[ASN][1000 genomes]
rs6697978	0.86[ASN][1000 genomes]
rs67026262	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67646822	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67876779	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68160001	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71652503	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72722469	0.85[ASN][1000 genomes]
rs72722475	0.85[ASN][1000 genomes]
rs72722484	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs72722498	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72724515	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72724555	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72724574	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72724586	0.83[EUR][1000 genomes]
rs72724587	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830603	chr1:93003657-93172206	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv1794348	chr1:93090476-93192932	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv1802611	chr1:93090476-93219907	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3790450	FAM69A	cis	Artery Tibial	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93014800-93100200	Weak transcription	Right Ventricle	heart
2	chr1:93026000-93091800	Weak transcription	Hela-S3	cervix
3	chr1:93052000-93119400	Weak transcription	NHEK	skin
4	chr1:93053600-93166200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:93055000-93100200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:93062000-93118800	Weak transcription	HMEC	breast
7	chr1:93063000-93100600	Weak transcription	Gastric	stomach
8	chr1:93064400-93100800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:93065200-93101000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:93065200-93118600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:93065800-93119600	Weak transcription	NH-A	brain
12	chr1:93066800-93103000	Weak transcription	NHDF-Ad	bronchial
13	chr1:93066800-93114600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:93067200-93101000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:93067400-93100800	Weak transcription	Brain Angular Gyrus	brain
16	chr1:93068200-93100600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:93068600-93100400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:93068600-93112600	Weak transcription	Brain Substantia Nigra	brain
19	chr1:93068800-93103200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:93069400-93104600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:93069600-93119600	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:93070000-93100800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:93070600-93100200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:93070600-93100600	Weak transcription	Colonic Mucosa	Colon
25	chr1:93070600-93101000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:93070800-93100800	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:93077200-93100600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:93078400-93096200	Weak transcription	Fetal Heart	heart
29	chr1:93080200-93100800	Weak transcription	Esophagus	oesophagus
30	chr1:93080800-93092600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr1:93081200-93100800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:93081200-93100800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:93082200-93101000	Weak transcription	HSMMtube	muscle
34	chr1:93082400-93101200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:93082600-93108600	Weak transcription	Psoas Muscle	Psoas
36	chr1:93082800-93100600	Weak transcription	Lung	lung
37	chr1:93082800-93100800	Weak transcription	Aorta	Aorta
38	chr1:93083400-93100400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:93083600-93101000	Weak transcription	Primary B cells from cord blood	blood
40	chr1:93083600-93101000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:93083600-93101000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:93083600-93106400	Weak transcription	Pancreas	Pancrea
43	chr1:93083800-93101000	Weak transcription	Fetal Kidney	kidney
44	chr1:93084000-93100800	Weak transcription	Left Ventricle	heart
45	chr1:93084000-93101000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:93084000-93101000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:93084200-93091200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr1:93084200-93100200	Weak transcription	Fetal Lung	lung
49	chr1:93084200-93100600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:93084200-93100600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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