Variant report

Variant	rs11578098
Chromosome Location	chr1:93119410-93119411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11164803	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs11164814	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164820	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11577426	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11578004	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs11581176	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11585590	0.84[EUR][1000 genomes]
rs11586570	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11588545	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11589122	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11589660	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11591094	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11800409	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11800771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11800848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11801763	0.88[YRI][hapmap]
rs11803097	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11804321	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11805007	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11805229	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11805698	0.89[EUR][1000 genomes]
rs11807962	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11808092	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11809055	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11809700	0.90[EUR][1000 genomes]
rs11810217	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12728322	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12730641	0.96[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12731107	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12733238	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12738833	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743005	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12743520	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12746893	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs12749480	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12749786	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12756698	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12756786	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1333743	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1415296	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1854797	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2051841	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2893226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34202284	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34221961	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34231012	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34244251	1.00[CHB][hapmap]
rs34250288	0.83[EUR][1000 genomes]
rs34305407	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34343030	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34734076	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34761380	0.91[EUR][1000 genomes]
rs34812295	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34843292	0.84[EUR][1000 genomes]
rs35038369	0.83[EUR][1000 genomes]
rs35241270	0.89[EUR][1000 genomes]
rs35311203	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35435370	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35526187	0.91[EUR][1000 genomes]
rs35612297	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35699160	0.82[EUR][1000 genomes]
rs35705463	0.83[EUR][1000 genomes]
rs35901796	0.83[EUR][1000 genomes]
rs36099538	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs36114576	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3790450	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]
rs4642892	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56044027	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6604026	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs67026262	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67646822	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67876779	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68160001	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71650502	0.80[ASN][1000 genomes]
rs71652503	0.91[EUR][1000 genomes]
rs72724515	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72724555	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72724574	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72724586	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72724587	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[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
rs11578098	FAM69A	cis	Artery Tibial	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93053600-93166200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:93065800-93119600	Weak transcription	NH-A	brain
3	chr1:93069600-93119600	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:93098400-93205400	Weak transcription	NHLF	lung
5	chr1:93101600-93120200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:93101600-93163600	Weak transcription	Colonic Mucosa	Colon
7	chr1:93101800-93119600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:93102000-93119800	Weak transcription	Brain Angular Gyrus	brain
9	chr1:93102000-93157600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:93110200-93120600	Weak transcription	Fetal Heart	heart
11	chr1:93111400-93119800	Weak transcription	Osteobl	bone
12	chr1:93112600-93120600	Weak transcription	Fetal Brain Male	brain
13	chr1:93114800-93119600	Weak transcription	Small Intestine	intestine
14	chr1:93114800-93121000	Weak transcription	HSMM	muscle
15	chr1:93115200-93120400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:93117200-93119600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:93117800-93119800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:93117800-93123600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:93118000-93119800	Strong transcription	Liver	Liver
20	chr1:93118200-93119800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:93118200-93119800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr1:93118200-93120000	Strong transcription	Stomach Smooth Muscle	stomach
23	chr1:93118400-93119600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:93118400-93120000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:93118400-93120000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
26	chr1:93118400-93120000	ZNF genes & repeats	Fetal Intestine Small	intestine
27	chr1:93118400-93120000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr1:93118400-93120000	ZNF genes & repeats	Fetal Stomach	stomach
29	chr1:93118600-93119600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:93118600-93119600	Strong transcription	Adipose Nuclei	Adipose
31	chr1:93118600-93119600	Strong transcription	Brain Anterior Caudate	brain
32	chr1:93118600-93119600	Strong transcription	Right Ventricle	heart
33	chr1:93118600-93119800	ZNF genes & repeats	Aorta	Aorta
34	chr1:93118600-93119800	Strong transcription	HSMMtube	muscle
35	chr1:93118600-93120000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:93118600-93120000	ZNF genes & repeats	Lung	lung
37	chr1:93118600-93120000	ZNF genes & repeats	Ovary	ovary
38	chr1:93118600-93120000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:93118600-93120200	ZNF genes & repeats	Fetal Muscle Leg	muscle
40	chr1:93118600-93122000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
41	chr1:93118600-93123400	ZNF genes & repeats	Fetal Intestine Large	intestine
42	chr1:93118600-93123800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
43	chr1:93118800-93119600	Strong transcription	Brain Substantia Nigra	brain
44	chr1:93118800-93119600	ZNF genes & repeats	Fetal Brain Female	brain
45	chr1:93118800-93119600	ZNF genes & repeats	Pancreas	Pancrea
46	chr1:93118800-93119600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr1:93118800-93119800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:93118800-93119800	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:93118800-93120000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:93118800-93120000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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