Variant report

Variant	rs11580229
Chromosome Location	chr1:227210820-227210821
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1045252	0.96[CEU][hapmap]
rs1045285	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1045286	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1045287	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1045289	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1045290	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10495273	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10916075	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11577007	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11578103	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11578479	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582863	0.82[ASN][1000 genomes]
rs11583229	0.99[ASN][1000 genomes]
rs11583489	1.00[CHB][hapmap]
rs11586604	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11587443	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11588904	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11589344	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1186	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12403236	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12403775	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs12405857	0.99[ASN][1000 genomes]
rs12406714	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12409230	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12409428	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12409755	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12410103	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12593	0.92[CEU][hapmap];0.93[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1319103	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs13376552	0.82[ASN][1000 genomes]
rs1343743	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1343744	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1343745	0.89[ASN][1000 genomes]
rs17528667	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17600627	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17600669	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17600725	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600747	0.99[ASN][1000 genomes]
rs17600947	0.99[ASN][1000 genomes]
rs1929855	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs1929862	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1929863	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1929864	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2104860	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183836	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2297412	0.92[CEU][hapmap]
rs2297415	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2297416	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2297418	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297419	0.89[ASN][1000 genomes]
rs34111989	0.82[ASN][1000 genomes]
rs3738729	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3768419	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs3768420	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs3768421	0.81[AMR][1000 genomes]
rs3768423	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3768424	0.81[AMR][1000 genomes]
rs3768425	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3795445	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3795446	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3795449	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3795451	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3795453	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146588	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs61834001	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61834004	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61834005	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61834006	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61834039	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6426558	0.81[AMR][1000 genomes]
rs6426559	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426560	0.99[ASN][1000 genomes]
rs6426584	0.86[CHB][hapmap]
rs6659424	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6664955	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6670924	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6677602	0.88[CEU][hapmap];0.93[CHB][hapmap]
rs6684821	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6690803	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6693535	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6699400	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6704144	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs68087483	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72748192	0.82[ASN][1000 genomes]
rs7355000	0.82[ASN][1000 genomes]
rs7520272	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7535826	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7549465	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7549586	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552783	0.84[AMR][1000 genomes]
rs7553837	1.00[CHB][hapmap]
rs7553990	0.82[ASN][1000 genomes]
rs7555621	0.94[ASN][1000 genomes]
rs9726097	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9727512	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1005811	chr1:227196502-227215967	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1007352	chr1:227196502-227247160	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv997751	chr1:227196502-227263537	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1010864	chr1:227199493-227246753	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1014423	chr1:227201253-227268843	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11580229	ADCK3	cis	Whole Blood	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:227176000-227216400	Weak transcription	NHLF	lung
4	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
5	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
6	chr1:227178600-227226200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:227179400-227215000	Weak transcription	Placenta	Placenta
8	chr1:227179600-227213800	Weak transcription	NH-A	brain
9	chr1:227182000-227216000	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:227182800-227224200	Weak transcription	Spleen	Spleen
11	chr1:227183200-227228200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:227183200-227240400	Weak transcription	Colonic Mucosa	Colon
13	chr1:227184000-227214600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:227184000-227234000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:227187200-227218600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:227190600-227217000	Weak transcription	Esophagus	oesophagus
17	chr1:227190600-227223200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:227190600-227272600	Weak transcription	Lung	lung
19	chr1:227191200-227214400	Weak transcription	Aorta	Aorta
20	chr1:227192600-227220200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:227192800-227214200	Weak transcription	Right Ventricle	heart
22	chr1:227192800-227220200	Weak transcription	Gastric	stomach
23	chr1:227202600-227217200	Strong transcription	Adipose Nuclei	Adipose
24	chr1:227202600-227222600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:227203000-227278800	Weak transcription	Pancreas	Pancrea
26	chr1:227204800-227214400	Weak transcription	Brain Substantia Nigra	brain
27	chr1:227205400-227216400	Weak transcription	HepG2	liver
28	chr1:227205600-227220400	Weak transcription	Stomach Mucosa	stomach
29	chr1:227206400-227211000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:227206600-227211000	Strong transcription	A549	lung
31	chr1:227206600-227212800	Strong transcription	K562	blood
32	chr1:227206600-227214400	Weak transcription	Brain Angular Gyrus	brain
33	chr1:227207400-227213800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:227207600-227211000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:227207600-227242000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:227208000-227211000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr1:227208200-227216200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:227208400-227211000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:227208400-227211000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:227208600-227216200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:227208800-227216200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:227208800-227222600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:227209000-227213400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:227209000-227214000	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:227209000-227214200	Weak transcription	Brain Germinal Matrix	brain
46	chr1:227209000-227214200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:227209000-227214200	Weak transcription	Fetal Heart	heart
48	chr1:227209000-227214200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:227209000-227214400	Weak transcription	Brain Anterior Caudate	brain
50	chr1:227209000-227215400	Weak transcription	Muscle Satellite Cultured Cells	--

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