Variant report

Variant	rs1530633
Chromosome Location	chr2:46590456-46590457
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46589429..46592507-chr2:46593401..46595603,3	K562	blood:
2	chr2:46541093..46544345-chr2:46588792..46591987,3	K562	blood:
3	chr2:46524125..46525936-chr2:46589569..46591167,2	K562	blood:
4	chr2:46586164..46589641-chr2:46590092..46593590,4	K562	blood:
5	chr2:46525172..46526736-chr2:46589773..46591531,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116016	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10191091	0.89[CEU][hapmap]
rs11675232	0.81[CEU][hapmap]
rs11692911	0.82[CEU][hapmap]
rs1530631	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1562452	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs1562453	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs2346176	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2881324	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs3754556	0.85[YRI][hapmap]
rs3768730	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4953356	0.96[CEU][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4953358	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4953359	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6544887	0.93[CEU][hapmap]
rs6544888	0.96[CEU][hapmap]
rs6544889	0.93[CEU][hapmap]
rs6544890	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6707241	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs6735812	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6740096	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6743991	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6756667	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7586141	0.81[EUR][1000 genomes]
rs7598371	0.81[CEU][hapmap]

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	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv916169	chr2:46310963-46622603	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46568000-46596600	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:46572600-46590600	Strong transcription	NHEK	skin
3	chr2:46573200-46613000	Strong transcription	Hela-S3	cervix
4	chr2:46573800-46591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:46574200-46590600	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr2:46574600-46607200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:46574800-46613000	Weak transcription	HSMM	muscle
8	chr2:46578800-46590800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:46580000-46594600	Weak transcription	Psoas Muscle	Psoas
10	chr2:46580600-46597200	Weak transcription	Fetal Heart	heart
11	chr2:46581200-46597000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:46583000-46591000	Weak transcription	Fetal Kidney	kidney
13	chr2:46583000-46591000	Strong transcription	Ovary	ovary
14	chr2:46583200-46591000	Strong transcription	Gastric	stomach
15	chr2:46584400-46591000	Weak transcription	K562	blood
16	chr2:46585000-46593200	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:46585200-46594600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:46585400-46592000	Weak transcription	Brain Substantia Nigra	brain
19	chr2:46585400-46593200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:46585400-46594000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:46585600-46592600	Weak transcription	Brain Anterior Caudate	brain
22	chr2:46585600-46593200	Weak transcription	Brain Angular Gyrus	brain
23	chr2:46586200-46591200	Strong transcription	HepG2	liver
24	chr2:46586600-46604000	Weak transcription	HSMMtube	muscle
25	chr2:46587200-46591000	Strong transcription	Aorta	Aorta
26	chr2:46587400-46590600	Genic enhancers	Left Ventricle	heart
27	chr2:46587400-46591000	Strong transcription	Fetal Stomach	stomach
28	chr2:46587400-46591200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:46587600-46591200	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:46587800-46591600	Strong transcription	HMEC	breast
31	chr2:46588400-46591000	Strong transcription	Pancreas	Pancrea
32	chr2:46588600-46591400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr2:46588600-46591400	Genic enhancers	NHLF	lung
34	chr2:46588600-46604800	Weak transcription	Stomach Mucosa	stomach
35	chr2:46588800-46596800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:46588800-46597200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:46588800-46598800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:46589000-46590600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:46589000-46591400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:46589000-46592200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr2:46589000-46592600	Enhancers	Primary T cells from cord blood	blood
42	chr2:46589000-46594800	Genic enhancers	Liver	Liver
43	chr2:46589200-46591000	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr2:46589200-46592200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr2:46589200-46593000	Genic enhancers	Adipose Nuclei	Adipose
46	chr2:46589200-46596200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:46589200-46597000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:46589400-46591000	Strong transcription	Lung	lung
49	chr2:46589400-46591000	Enhancers	Osteobl	bone
50	chr2:46589400-46592200	Enhancers	Primary T helper naive cells from peripheral blood	blood

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