Variant report

Variant	rs399628
Chromosome Location	chr1:45435492-45435493
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45283589..45286724-chr1:45434878..45437346,4	K562	blood:
2	chr1:45430652..45433311-chr1:45435408..45437709,2	K562	blood:
3	chr1:45430652..45433311-chr1:45435078..45437709,3	K562	blood:

Variant related genes	Relation type
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1226572	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263965	0.86[ASN][1000 genomes]
rs263966	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263975	0.81[ASN][1000 genomes]
rs263977	0.81[ASN][1000 genomes]
rs263980	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263982	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs263987	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263990	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263998	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs264005	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs264009	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs264011	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs264014	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3121173	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36107413	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs398200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401665	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs438493	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs452989	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs489676	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61789958	0.86[ASN][1000 genomes]
rs620764	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs659293	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9429058	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45389200-45450200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:45391200-45438400	Weak transcription	Dnd41	blood
3	chr1:45391200-45439800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:45391400-45437200	Weak transcription	Fetal Thymus	thymus
5	chr1:45392800-45443200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:45397800-45435800	Weak transcription	Primary B cells from cord blood	blood
7	chr1:45407600-45438400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:45412000-45440000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:45412800-45441000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:45413200-45436200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:45413400-45437800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:45413400-45439600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:45413400-45439800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:45413400-45441400	Weak transcription	Brain Anterior Caudate	brain
15	chr1:45413600-45441400	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:45413600-45442800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:45413800-45437600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:45413800-45438400	Weak transcription	Right Ventricle	heart
19	chr1:45413800-45439800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:45413800-45441600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:45414000-45435600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:45414000-45436200	Weak transcription	Ovary	ovary
23	chr1:45414000-45438400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:45414000-45439400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:45414000-45439600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:45414000-45440000	Weak transcription	Brain Angular Gyrus	brain
27	chr1:45414000-45440000	Weak transcription	Fetal Lung	lung
28	chr1:45414000-45441000	Weak transcription	Fetal Kidney	kidney
29	chr1:45414000-45441600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:45414000-45443200	Weak transcription	Pancreas	Pancrea
31	chr1:45414000-45450800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:45414000-45451000	Weak transcription	Spleen	Spleen
33	chr1:45414200-45443000	Weak transcription	Gastric	stomach
34	chr1:45415000-45437200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:45415400-45438600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:45415600-45440400	Weak transcription	Fetal Brain Female	brain
37	chr1:45416600-45443600	Weak transcription	Psoas Muscle	Psoas
38	chr1:45417600-45442000	Weak transcription	Placenta	Placenta
39	chr1:45421000-45450800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:45421400-45443400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:45422000-45441400	Weak transcription	Esophagus	oesophagus
42	chr1:45423400-45439600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:45423600-45441400	Weak transcription	NHLF	lung
44	chr1:45424000-45435600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:45424200-45440800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:45424600-45436000	Weak transcription	Adipose Nuclei	Adipose
47	chr1:45424600-45438400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:45424600-45439000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:45424600-45439400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:45424600-45441400	Weak transcription	Lung	lung

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