Variant report

Variant	rs263980
Chromosome Location	chr1:45390051-45390052
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45389689..45392269-chr1:45413336..45415947,2	K562	blood:
2	chr1:45185888..45187601-chr1:45389405..45391637,2	K562	blood:
3	chr1:45386176..45391907-chr1:45393565..45396942,5	K562	blood:

Variant related genes	Relation type
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10158188	0.80[ASN][1000 genomes]
rs11211044	0.80[ASN][1000 genomes]
rs11211046	0.82[ASN][1000 genomes]
rs11211047	0.82[ASN][1000 genomes]
rs12094007	0.82[ASN][1000 genomes]
rs12120470	0.82[ASN][1000 genomes]
rs1226572	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12408818	0.82[ASN][1000 genomes]
rs12568071	0.82[ASN][1000 genomes]
rs263962	0.84[ASN][1000 genomes]
rs263965	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs263966	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263975	0.86[ASN][1000 genomes]
rs263977	0.86[ASN][1000 genomes]
rs263982	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs263987	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263990	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263998	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs264005	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs264009	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs264011	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs264014	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3121173	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36107413	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398200	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs399628	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs401665	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs438493	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452989	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs489676	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61789958	0.92[ASN][1000 genomes]
rs620764	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs659293	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6688465	0.82[ASN][1000 genomes]
rs6696675	0.82[ASN][1000 genomes]
rs6698951	0.82[ASN][1000 genomes]
rs746320	0.82[ASN][1000 genomes]
rs932691	0.82[ASN][1000 genomes]
rs9429058	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9988451	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45347600-45410800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:45350800-45411800	Weak transcription	Left Ventricle	heart
3	chr1:45355800-45411200	Weak transcription	Fetal Lung	lung
4	chr1:45356000-45407000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr1:45356000-45423800	Weak transcription	Thymus	Thymus
6	chr1:45356400-45390600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:45357400-45390600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:45357400-45411800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:45357600-45391600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:45357800-45391000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:45358200-45396800	Weak transcription	Fetal Intestine Small	intestine
12	chr1:45359000-45411800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:45359200-45390200	Weak transcription	HSMM	muscle
14	chr1:45359200-45390600	Weak transcription	Dnd41	blood
15	chr1:45359200-45396800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:45359200-45423600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:45360600-45410000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:45360800-45390400	Weak transcription	HMEC	breast
19	chr1:45360800-45396800	Weak transcription	Primary B cells from cord blood	blood
20	chr1:45362200-45390400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:45362200-45424200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:45362400-45390800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:45362400-45397000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:45362800-45390200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:45362800-45390800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:45363200-45390600	Weak transcription	Primary T cells from cord blood	blood
27	chr1:45363200-45390800	Weak transcription	Liver	Liver
28	chr1:45369400-45390400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:45369400-45390800	Weak transcription	HSMMtube	muscle
30	chr1:45369400-45396800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:45369600-45390400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:45373000-45411600	Weak transcription	HepG2	liver
33	chr1:45374400-45396600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:45374600-45392000	Weak transcription	Adipose Nuclei	Adipose
35	chr1:45375200-45411800	Weak transcription	Aorta	Aorta
36	chr1:45376800-45390600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:45377200-45392200	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:45378200-45390600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:45378200-45412000	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:45378400-45396600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:45378600-45412200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:45379200-45390400	Weak transcription	K562	blood
43	chr1:45379800-45390200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:45380000-45390600	Weak transcription	Fetal Thymus	thymus
45	chr1:45381400-45392000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:45384600-45412600	Weak transcription	Psoas Muscle	Psoas
47	chr1:45384800-45406800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:45385400-45390200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:45386200-45406600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr1:45386400-45411600	Weak transcription	Fetal Kidney	kidney

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