Variant report

Variant	rs489676
Chromosome Location	chr1:45452227-45452228
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45451325..45453836-chr1:45473269..45474967,2	MCF-7	breast:
2	chr1:45451300..45453679-chr1:45476530..45479236,3	MCF-7	breast:
3	chr1:45186235..45188904-chr1:45452213..45453975,2	K562	blood:
4	chr1:45194988..45198272-chr1:45451491..45453905,3	K562	blood:
5	chr1:45450854..45457330-chr1:45465047..45472849,14	K562	blood:
6	chr1:45449901..45454181-chr1:45475970..45480540,16	K562	blood:
7	chr1:45283976..45287622-chr1:45450715..45458034,11	K562	blood:
8	chr1:45284059..45286396-chr1:45450000..45452623,4	MCF-7	breast:
9	chr1:45282917..45288387-chr1:45449365..45456835,12	K562	blood:
10	chr1:45239905..45242727-chr1:45449975..45452356,2	K562	blood:
11	chr1:45273964..45275771-chr1:45451640..45453619,2	K562	blood:
12	chr1:45450947..45453129-chr1:45770139..45772507,2	K562	blood:
13	chr1:45271433..45273539-chr1:45450490..45453055,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000126088	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000126107	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10890319	0.80[AFR][1000 genomes]
rs12047556	0.80[AFR][1000 genomes]
rs1226572	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2298006	0.82[AFR][1000 genomes]
rs263965	0.84[ASN][1000 genomes]
rs263966	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs263980	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs263982	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs263987	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263990	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263998	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs264005	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs264009	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs264011	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs264014	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3121173	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36107413	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs398200	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs399628	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs401665	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs438493	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs452989	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61789958	0.85[ASN][1000 genomes]
rs620764	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs659293	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6671633	0.80[AFR][1000 genomes]
rs7537361	0.80[AFR][1000 genomes]
rs9429058	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	esv2830314	chr1:45430218-45455285	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45451000-45452800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr1:45451000-45452800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:45451000-45452800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:45451000-45452800	Active TSS	HSMMtube	muscle
5	chr1:45451000-45453200	Active TSS	A549	lung
6	chr1:45451200-45452600	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:45451200-45452600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr1:45451200-45452800	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr1:45451200-45452800	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr1:45451200-45452800	Active TSS	NHDF-Ad	bronchial
11	chr1:45451400-45452400	Active TSS	GM12878-XiMat	blood
12	chr1:45451400-45452600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr1:45451400-45452600	Active TSS	Aorta	Aorta
14	chr1:45451400-45452800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr1:45451400-45452800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:45451400-45452800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:45451400-45452800	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr1:45451400-45452800	Active TSS	NHLF	lung
19	chr1:45451600-45452400	Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr1:45451600-45452400	Active TSS	Muscle Satellite Cultured Cells	--
21	chr1:45451600-45452400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:45451600-45452400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:45451600-45452400	Active TSS	Esophagus	oesophagus
24	chr1:45451600-45452400	Active TSS	Fetal Intestine Small	intestine
25	chr1:45451600-45452400	Active TSS	Fetal Muscle Trunk	muscle
26	chr1:45451600-45452400	Active TSS	Placenta Amnion	Placenta Amnion
27	chr1:45451600-45452400	Active TSS	Small Intestine	intestine
28	chr1:45451600-45452400	Active TSS	Stomach Smooth Muscle	stomach
29	chr1:45451600-45452600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:45451600-45452600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:45451600-45452600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:45451600-45452600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:45451600-45452600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:45451600-45452600	Active TSS	Colon Smooth Muscle	Colon
35	chr1:45451600-45452600	Active TSS	Gastric	stomach
36	chr1:45451600-45452600	Active TSS	Lung	lung
37	chr1:45451600-45452600	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr1:45451600-45452600	Active TSS	Spleen	Spleen
39	chr1:45451600-45452800	Active TSS	H1 Cell Line	embryonic stem cell
40	chr1:45451600-45452800	Active TSS	H9 Cell Line	embryonic stem cell
41	chr1:45451600-45452800	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr1:45451600-45452800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:45451600-45452800	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr1:45451600-45452800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:45451600-45452800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:45451600-45452800	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr1:45451600-45452800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:45451600-45452800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:45451600-45452800	Active TSS	Brain Anterior Caudate	brain
50	chr1:45451600-45452800	Active TSS	Brain Cingulate Gyrus	brain

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