Variant report

Variant	rs12027783
Chromosome Location	chr1:153937864-153937865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153937593-153937999	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153936330..153941464-chr1:154191669..154195552,8	MCF-7	breast:
2	chr1:153605540..153608540-chr1:153937612..153940414,3	MCF-7	breast:
3	chr1:153936098..153938705-chr1:154152746..154155431,3	MCF-7	breast:
4	chr1:153641625..153644878-chr1:153937648..153941391,3	K562	blood:
5	chr1:153742918..153749628-chr1:153933334..153942122,16	MCF-7	breast:
6	chr1:153580618..153585586-chr1:153936399..153942199,7	MCF-7	breast:
7	chr1:153640832..153646304-chr1:153937039..153940655,5	MCF-7	breast:
8	chr1:153747310..153750060-chr1:153937716..153939765,3	MCF-7	breast:

No data

Variant related genes	Relation type
CREB3L4	TF binding region
ENSG00000273026	TF binding region
SLC39A1	TF binding region
ENSG00000143612	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000160679	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10127983	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1043608	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10559	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10796968	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10908557	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908558	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1110165	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11264532	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11264559	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11264567	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264619	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11264620	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11264680	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264734	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11264743	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264763	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11577942	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11581644	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11583152	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11583896	0.82[AFR][1000 genomes]
rs11585416	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11586075	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11586593	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11586830	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11587151	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11589043	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11589857	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11590099	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11591134	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12022158	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12022730	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12023699	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12028398	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12032914	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12033835	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12038577	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12041850	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12041920	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12042562	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12042989	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12043350	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12401565	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12403956	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12406003	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12409811	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12567313	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1547766	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1547767	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1572788	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34805562	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3748848	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3748849	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3791187	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4363451	0.80[AFR][1000 genomes]
rs4508047	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4520447	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4595397	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4612664	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845357	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845358	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845576	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845578	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845583	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845585	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58095661	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59308681	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59678326	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60150125	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61219911	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6427329	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6659220	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6666703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671132	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6680140	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6694061	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6700451	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6724	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72694220	0.80[AFR][1000 genomes]
rs72694231	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs72694234	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7524739	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7537691	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552274	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8450	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs946682	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9660089	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv532552	chr1:153912047-153950752	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153935200-153938400	Active TSS	Hela-S3	cervix
2	chr1:153936800-153938400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:153936800-153938400	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr1:153936800-153938400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:153936800-153938400	Weak transcription	Fetal Heart	heart
6	chr1:153936800-153939200	Weak transcription	Aorta	Aorta
7	chr1:153936800-153939200	Weak transcription	Ovary	ovary
8	chr1:153936800-153939600	Weak transcription	Gastric	stomach
9	chr1:153936800-153939600	Weak transcription	Small Intestine	intestine
10	chr1:153937000-153938000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:153937000-153938000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr1:153937000-153938200	Enhancers	Primary T cells from cord blood	blood
13	chr1:153937000-153938400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr1:153937000-153938400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:153937000-153938400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:153937000-153938400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:153937000-153938400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:153937000-153938400	Weak transcription	Colonic Mucosa	Colon
19	chr1:153937000-153938400	Enhancers	Fetal Thymus	thymus
20	chr1:153937000-153938400	Weak transcription	NHDF-Ad	bronchial
21	chr1:153937000-153938600	Enhancers	Primary B cells from cord blood	blood
22	chr1:153937000-153938600	Weak transcription	Adipose Nuclei	Adipose
23	chr1:153937000-153938600	Weak transcription	Brain Anterior Caudate	brain
24	chr1:153937000-153938600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:153937000-153938600	Weak transcription	Fetal Kidney	kidney
26	chr1:153937000-153938600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:153937000-153938600	Weak transcription	Pancreas	Pancrea
28	chr1:153937000-153938600	Weak transcription	HSMMtube	muscle
29	chr1:153937000-153938800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:153937000-153938800	Weak transcription	Right Atrium	heart
31	chr1:153937000-153939000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:153937000-153939000	Enhancers	Primary B cells from peripheral blood	blood
33	chr1:153937000-153939000	Weak transcription	Brain Angular Gyrus	brain
34	chr1:153937000-153939000	Weak transcription	Brain Substantia Nigra	brain
35	chr1:153937000-153939200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr1:153937000-153939200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:153937000-153939200	Enhancers	Fetal Brain Male	brain
38	chr1:153937000-153939400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:153937000-153939600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:153937000-153939600	Weak transcription	Esophagus	oesophagus
41	chr1:153937200-153938000	Enhancers	NHEK	skin
42	chr1:153937200-153938200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:153937200-153938200	Weak transcription	Thymus	Thymus
44	chr1:153937200-153938400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:153937200-153938400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:153937200-153938400	Weak transcription	Liver	Liver
47	chr1:153937200-153938400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:153937200-153938400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:153937200-153938400	Weak transcription	Fetal Brain Female	brain
50	chr1:153937200-153938400	Weak transcription	Rectal Mucosa Donor 31	rectum

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