Variant report

Variant	rs11580020
Chromosome Location	chr1:228880466-228880467
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228880153-228880524	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228878069..228881022-chr1:228881765..228883502,2	MCF-7	breast:

Variant related genes	Relation type
RHOU	TF binding region
ENSG00000116574	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1062060	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs11578216	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs11583565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585206	0.95[CEU][hapmap]
rs11587994	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11803118	0.95[CEU][hapmap]
rs17352535	0.85[CEU][hapmap]
rs17352654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17352829	0.93[ASN][1000 genomes]
rs3738073	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41270187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41270189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271473	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4391638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4641285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4993975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55730631	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55956922	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56221905	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61825705	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6665334	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6701241	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72751907	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72751929	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72751931	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013051	chr1:228786702-228903706	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv997801	chr1:228786702-228975127	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv870365	chr1:228788356-229267904	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription 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	14 gene(s)	inside rSNPs	diseases
4	nsv998255	chr1:228791784-228919202	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv549299	chr1:228793246-229455876	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv468316	chr1:228854703-228919202	Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv549300	chr1:228854703-228919202	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11580020	MIXL1	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228872600-228880600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:228872600-228881200	Weak transcription	Esophagus	oesophagus
3	chr1:228872600-228884400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr1:228873200-228884800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:228873800-228882800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:228873800-228884200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:228873800-228884200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:228874000-228881800	Genic enhancers	Liver	Liver
9	chr1:228874400-228884000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:228875000-228881000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr1:228875000-228884200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:228875600-228883200	Strong transcription	Duodenum Mucosa	Duodenum
13	chr1:228875800-228881000	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:228875800-228884000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:228876200-228883200	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr1:228876600-228882600	Strong transcription	Placenta	Placenta
17	chr1:228876600-228883400	Strong transcription	Fetal Intestine Small	intestine
18	chr1:228876800-228884800	Weak transcription	Fetal Brain Male	brain
19	chr1:228877000-228883200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr1:228877000-228884800	Weak transcription	Fetal Kidney	kidney
21	chr1:228877200-228880800	Strong transcription	Fetal Intestine Large	intestine
22	chr1:228877200-228883600	Strong transcription	Fetal Stomach	stomach
23	chr1:228877200-228889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:228877400-228883800	Strong transcription	Fetal Brain Female	brain
25	chr1:228877600-228881200	Strong transcription	Colon Smooth Muscle	Colon
26	chr1:228877600-228881600	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:228877600-228883600	Strong transcription	Fetal Muscle Leg	muscle
28	chr1:228877800-228881000	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:228877800-228881200	Strong transcription	Primary T cells from cord blood	blood
30	chr1:228878000-228881000	Strong transcription	Rectal Smooth Muscle	rectum
31	chr1:228878000-228881000	Strong transcription	HepG2	liver
32	chr1:228878000-228881600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:228878000-228881800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr1:228878000-228881800	Strong transcription	Lung	lung
35	chr1:228878000-228881800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:228878000-228882800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:228878000-228883200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:228878200-228880800	Strong transcription	Spleen	Spleen
39	chr1:228878200-228883000	Strong transcription	Adipose Nuclei	Adipose
40	chr1:228878200-228883000	Strong transcription	Aorta	Aorta
41	chr1:228878400-228880600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:228878400-228881000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:228878400-228881600	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr1:228878600-228881000	Strong transcription	Colonic Mucosa	Colon
45	chr1:228878600-228883000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:228878800-228880800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:228878800-228881200	Genic enhancers	Brain Cingulate Gyrus	brain
48	chr1:228878800-228881600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:228878800-228882600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr1:228878800-228883000	Strong transcription	Fetal Lung	lung

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