Variant report

Variant	rs5009460
Chromosome Location	chr15:42838047-42838048
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42837304..42838910-chr15:42839465..42842272,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137814	Chromatin interaction
ENSG00000180979	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1044866	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11541527	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16973349	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36090286	0.85[AFR][1000 genomes]
rs57249373	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57349778	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58122107	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58562675	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58952814	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59058205	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59091063	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60060355	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60168929	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60606292	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60697170	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60839827	1.00[AMR][1000 genomes]
rs61368952	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61474811	0.85[AMR][1000 genomes]
rs6493048	0.92[AFR][1000 genomes]
rs6493049	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6493050	0.95[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7166143	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7166633	0.87[AMR][1000 genomes]
rs7172064	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7172955	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7173155	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7175059	1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs7178822	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7181938	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73402762	0.85[AMR][1000 genomes]
rs73402776	0.85[AMR][1000 genomes]
rs73402796	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73404708	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404711	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404725	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404729	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404746	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404754	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73404758	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404768	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404774	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404793	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406526	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406531	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406544	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406553	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406557	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs768118	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8023948	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8027207	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8031383	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8031883	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8033555	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8033810	1.00[AMR][1000 genomes]
rs8034001	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8035877	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8036927	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs8037277	0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8040624	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42797400-42839800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:42797600-42839400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:42799200-42839400	Weak transcription	Stomach Mucosa	stomach
4	chr15:42802400-42839200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:42803600-42839400	Weak transcription	A549	lung
6	chr15:42806200-42839000	Weak transcription	Fetal Brain Male	brain
7	chr15:42808400-42839000	Weak transcription	Fetal Heart	heart
8	chr15:42810200-42840200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42817400-42840200	Weak transcription	Pancreas	Pancrea
10	chr15:42821200-42839800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:42822200-42840200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:42822800-42840000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:42823400-42840200	Weak transcription	Psoas Muscle	Psoas
14	chr15:42824000-42840200	Weak transcription	Small Intestine	intestine
15	chr15:42824400-42839400	Weak transcription	Brain Substantia Nigra	brain
16	chr15:42824600-42838400	Weak transcription	HepG2	liver
17	chr15:42824600-42839600	Weak transcription	Right Ventricle	heart
18	chr15:42831200-42839000	Strong transcription	Fetal Lung	lung
19	chr15:42831400-42839200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:42831600-42839000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:42831600-42840200	Weak transcription	Gastric	stomach
22	chr15:42833400-42838200	Strong transcription	Placenta	Placenta
23	chr15:42833400-42838400	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr15:42834400-42839200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr15:42834400-42839400	Strong transcription	Fetal Muscle Leg	muscle
26	chr15:42834600-42838200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:42834600-42838400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:42834600-42838400	Strong transcription	Liver	Liver
29	chr15:42834800-42838200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr15:42834800-42838600	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:42834800-42838800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr15:42835000-42838200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:42835000-42838400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:42835000-42839000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr15:42835000-42839200	Strong transcription	Fetal Thymus	thymus
36	chr15:42835800-42838200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr15:42835800-42838200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:42835800-42838400	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr15:42835800-42838600	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr15:42836400-42838200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:42836400-42838200	Weak transcription	Colon Smooth Muscle	Colon
42	chr15:42836600-42838200	Weak transcription	NH-A	brain
43	chr15:42836600-42839200	Weak transcription	Brain Anterior Caudate	brain
44	chr15:42836600-42839400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:42836800-42838800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr15:42836800-42839200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr15:42836800-42839200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr15:42837000-42838600	Strong transcription	Fetal Kidney	kidney
49	chr15:42837000-42839200	Weak transcription	Fetal Intestine Small	intestine
50	chr15:42837000-42839400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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