Variant report

Variant	rs1875529
Chromosome Location	chr5:98369054-98369055
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98234770..98237007-chr5:98368052..98370325,2	MCF-7	breast:
2	chr5:98362205..98363958-chr5:98366950..98369649,2	MCF-7	breast:
3	chr5:97966444..97968012-chr5:98368423..98370387,2	K562	blood:
4	chr5:98261108..98266251-chr5:98365242..98369850,9	K562	blood:

Variant related genes	Relation type
ENSG00000153922	Chromatin interaction
ENSG00000248489	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10040066	1.00[CHB][hapmap]
rs10041261	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10050804	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10076291	0.92[ASN][1000 genomes]
rs10477857	0.82[AMR][1000 genomes]
rs10479345	0.92[ASN][1000 genomes]
rs10479346	0.92[ASN][1000 genomes]
rs10479348	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11242567	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11242574	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745405	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949103	0.92[ASN][1000 genomes]
rs11950452	0.92[ASN][1000 genomes]
rs11950855	0.87[ASN][1000 genomes]
rs11960896	0.92[ASN][1000 genomes]
rs12109067	1.00[ASN][1000 genomes]
rs12189335	0.92[ASN][1000 genomes]
rs12515042	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13179812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1393210	1.00[ASN][1000 genomes]
rs1472622	1.00[CHB][hapmap]
rs151102	1.00[CHB][hapmap]
rs1604450	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161729	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs161730	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs161731	1.00[CHB][hapmap]
rs161732	1.00[CHB][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes]
rs161935	1.00[CHB][hapmap]
rs161936	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs167798	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2221268	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs246251	0.80[AMR][1000 genomes]
rs325195	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs325220	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs326480	1.00[CHB][hapmap]
rs326481	1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs326482	1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs327807	1.00[CHB][hapmap]
rs34488	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34489	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs34496	1.00[CHB][hapmap]
rs34498	1.00[CHB][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs366353	1.00[CHB][hapmap];0.81[GIH][hapmap]
rs39660	0.84[AMR][1000 genomes]
rs40075	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs4343864	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4448016	1.00[ASN][1000 genomes]
rs4565239	1.00[CHB][hapmap]
rs4583911	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs467728	1.00[CHB][hapmap]
rs4703052	0.92[ASN][1000 genomes]
rs4703340	0.92[ASN][1000 genomes]
rs4703345	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs539024	1.00[CHB][hapmap]
rs6865618	1.00[ASN][1000 genomes]
rs6878136	1.00[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6885458	1.00[ASN][1000 genomes]
rs709386	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs709387	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs709388	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs709389	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7449447	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7712408	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7719562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719649	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723242	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs819227	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs819230	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs819231	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024391	chr5:98355665-98653657	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv599118	chr5:98358191-99029453	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv599119	chr5:98358191-99315677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98366200-98369400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:98368000-98370200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr5:98368200-98369200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:98368200-98369200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:98368200-98369800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr5:98368200-98369800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr5:98368200-98370200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr5:98368200-98370400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:98368400-98369200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr5:98368400-98369200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:98368400-98369200	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr5:98368400-98369200	Flanking Active TSS	Fetal Intestine Small	intestine
13	chr5:98368400-98369200	Flanking Active TSS	Fetal Lung	lung
14	chr5:98368400-98369200	Flanking Active TSS	NHDF-Ad	bronchial
15	chr5:98368400-98369400	Active TSS	Brain Substantia Nigra	brain
16	chr5:98368400-98369400	Active TSS	Stomach Smooth Muscle	stomach
17	chr5:98368400-98369400	Active TSS	HepG2	liver
18	chr5:98368400-98369600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:98368400-98369600	Active TSS	Colon Smooth Muscle	Colon
20	chr5:98368400-98369600	Active TSS	Left Ventricle	heart
21	chr5:98368400-98369600	Active TSS	Rectal Smooth Muscle	rectum
22	chr5:98368400-98369600	Active TSS	Right Atrium	heart
23	chr5:98368400-98369600	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr5:98368400-98369600	Flanking Active TSS	Dnd41	blood
25	chr5:98368400-98369600	Flanking Active TSS	GM12878-XiMat	blood
26	chr5:98368400-98369600	Flanking Active TSS	HUVEC	blood vessel
27	chr5:98368400-98369600	Flanking Active TSS	Osteobl	bone
28	chr5:98368400-98369800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr5:98368400-98369800	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr5:98368400-98369800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr5:98368400-98370000	Enhancers	Small Intestine	intestine
32	chr5:98368400-98370200	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr5:98368400-98370400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:98368600-98369200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:98368600-98369200	Flanking Active TSS	Hela-S3	cervix
36	chr5:98368600-98369400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr5:98368600-98369400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:98368600-98369600	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr5:98368600-98369600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr5:98368600-98369600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr5:98368600-98369800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr5:98368600-98370000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr5:98368800-98369200	Active TSS	Colonic Mucosa	Colon
44	chr5:98368800-98369200	Flanking Active TSS	Fetal Intestine Large	intestine
45	chr5:98368800-98369200	Active TSS	A549	lung
46	chr5:98368800-98369200	Active TSS	HSMM	muscle
47	chr5:98368800-98369200	Flanking Active TSS	HSMMtube	muscle
48	chr5:98368800-98369400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:98368800-98369400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:98368800-98369400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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