Variant report

Variant	rs2918416
Chromosome Location	chr5:142741027-142741028
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	chr5:142712062..142716024-chr5:142739998..142742842,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231579	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10052957	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10482633	0.85[GIH][hapmap]
rs10482642	0.81[GIH][hapmap]
rs10482689	0.81[GIH][hapmap]
rs10515521	0.85[GIH][hapmap]
rs11740792	0.85[GIH][hapmap]
rs11747997	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11749561	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1438732	1.00[JPT][hapmap]
rs1635474	0.80[ASN][1000 genomes]
rs17339831	0.88[GIH][hapmap]
rs1837262	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1866388	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs190488	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2043840	1.00[JPT][hapmap]
rs258750	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs258753	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.82[ASN][1000 genomes]
rs258754	0.82[ASN][1000 genomes]
rs258755	0.82[ASN][1000 genomes]
rs258763	0.80[AFR][1000 genomes]
rs258813	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs258814	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2918415	1.00[JPT][hapmap]
rs2918417	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2918418	1.00[JPT][hapmap]
rs2918419	1.00[JPT][hapmap]
rs2963149	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2963151	1.00[JPT][hapmap]
rs2963153	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2963154	1.00[JPT][hapmap]
rs33380	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs33389	1.00[JPT][hapmap]
rs4128428	0.85[GIH][hapmap]
rs6188	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6194	1.00[JPT][hapmap]
rs6196	1.00[JPT][hapmap]
rs6198	0.85[GIH][hapmap]
rs6861962	1.00[JPT][hapmap]
rs712189	0.86[JPT][hapmap]
rs72801096	0.95[ASN][1000 genomes]
rs852975	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs852977	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs852978	1.00[JPT][hapmap]
rs852979	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs852982	0.87[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs853154	0.83[ASN][1000 genomes]
rs853157	0.85[JPT][hapmap]
rs853177	0.85[ASN][1000 genomes]
rs853178	0.85[ASN][1000 genomes]
rs853184	1.00[JPT][hapmap]
rs860457	0.87[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs860465	0.85[ASN][1000 genomes]
rs862489	0.85[ASN][1000 genomes]
rs864082	1.00[JPT][hapmap]
rs9324918	1.00[JPT][hapmap]

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	nsv1023976	chr5:142692062-142813664	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142693800-142747400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:142725000-142764200	Weak transcription	Lung	lung
3	chr5:142733800-142742000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:142734000-142743000	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr5:142734000-142756400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:142734200-142742200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:142734200-142743600	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr5:142734200-142743600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr5:142734200-142754200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:142735600-142742400	Weak transcription	Left Ventricle	heart
11	chr5:142735600-142743000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:142735600-142743600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:142735600-142743600	Weak transcription	HSMM	muscle
14	chr5:142735600-142743800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr5:142735600-142756000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:142735800-142748200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:142735800-142751200	Weak transcription	HMEC	breast
18	chr5:142735800-142751800	Weak transcription	NHEK	skin
19	chr5:142736200-142741600	Weak transcription	Fetal Muscle Leg	muscle
20	chr5:142736200-142741800	Weak transcription	Right Atrium	heart
21	chr5:142736200-142742200	Weak transcription	Ovary	ovary
22	chr5:142736200-142746200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:142736200-142748200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:142736200-142755800	Weak transcription	Small Intestine	intestine
25	chr5:142736200-142756000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr5:142736800-142746800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:142737000-142745200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr5:142737200-142742600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:142738000-142742200	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr5:142738200-142742000	Enhancers	A549	lung
31	chr5:142738400-142742800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:142738800-142741400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr5:142738800-142742200	Enhancers	Dnd41	blood
34	chr5:142738800-142742400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr5:142738800-142744000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr5:142739200-142741800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:142739200-142742400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr5:142739400-142741200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:142739400-142741400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:142739400-142763600	Weak transcription	Thymus	Thymus
41	chr5:142739600-142741200	Flanking Active TSS	GM12878-XiMat	blood
42	chr5:142739600-142741800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:142739600-142742400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr5:142739600-142754200	Weak transcription	Fetal Thymus	thymus
45	chr5:142739800-142741200	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr5:142739800-142741800	Enhancers	Primary T cells from cord blood	blood
47	chr5:142739800-142741800	Enhancers	Fetal Lung	lung
48	chr5:142739800-142743400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr5:142739800-142743600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr5:142740000-142741400	Enhancers	Duodenum Smooth Muscle	Duodenum

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