Variant report

Variant	rs72678900
Chromosome Location	chr1:59399218-59399219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59244053..59249750-chr1:59393075..59399809,12	K562	blood:
2	chr1:59246732..59251125-chr1:59394532..59399253,8	MCF-7	breast:
3	chr1:59244308..59248659-chr1:59395754..59399809,6	K562	blood:
4	chr1:59392641..59396388-chr1:59399124..59401431,3	K562	blood:
5	chr1:59388758..59390537-chr1:59398556..59401033,2	K562	blood:

Variant related genes	Relation type
ENSG00000177606	Chromatin interaction
ENSG00000234807	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12071047	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12089816	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12093908	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17096897	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17118423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118430	0.81[EUR][1000 genomes]
rs17118441	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1886744	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477743	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764909	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35393496	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55675910	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55834295	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55872264	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56175432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56219110	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56251271	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56349902	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58558886	0.82[EUR][1000 genomes]
rs66555203	0.82[EUR][1000 genomes]
rs6681035	0.81[EUR][1000 genomes]
rs72678885	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72678896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678899	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678901	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680106	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680107	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680109	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680113	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72921571	0.97[EUR][1000 genomes];1.00[ASN][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	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv546316	chr1:59368947-59457815	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59386600-59399800	Enhancers	Fetal Intestine Small	intestine
2	chr1:59389000-59407000	Weak transcription	Spleen	Spleen
3	chr1:59389200-59401400	Weak transcription	Left Ventricle	heart
4	chr1:59390200-59399600	Enhancers	Placenta Amnion	Placenta Amnion
5	chr1:59391200-59399600	Enhancers	Fetal Intestine Large	intestine
6	chr1:59392000-59399600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:59392600-59399400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:59393600-59400800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:59393600-59406800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:59395800-59400000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:59396000-59400400	Enhancers	Hela-S3	cervix
12	chr1:59396600-59399800	Enhancers	HMEC	breast
13	chr1:59397200-59399400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:59397600-59399400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr1:59397600-59399400	Enhancers	NHDF-Ad	bronchial
16	chr1:59397600-59399600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:59397600-59399600	Enhancers	Osteobl	bone
18	chr1:59397800-59399400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:59397800-59399400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:59397800-59399400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:59397800-59399400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:59397800-59399600	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr1:59397800-59399600	Enhancers	NHLF	lung
24	chr1:59398000-59399400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:59398000-59399600	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr1:59398200-59399600	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr1:59398200-59399600	Enhancers	Duodenum Mucosa	Duodenum
28	chr1:59398200-59399800	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr1:59398400-59399400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:59398400-59399400	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr1:59398400-59399400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:59398400-59399400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:59398400-59399400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr1:59398400-59399400	Enhancers	HepG2	liver
35	chr1:59398400-59399600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr1:59398400-59399600	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr1:59398600-59399400	Enhancers	Primary B cells from peripheral blood	blood
38	chr1:59398600-59399400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr1:59398600-59399400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr1:59398600-59399400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr1:59398600-59399400	Enhancers	Fetal Lung	lung
42	chr1:59398600-59399400	Enhancers	Gastric	stomach
43	chr1:59398600-59399400	Enhancers	Small Intestine	intestine
44	chr1:59398600-59399600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:59398800-59399400	Flanking Active TSS	A549	lung
46	chr1:59398800-59400400	Enhancers	Stomach Mucosa	stomach
47	chr1:59398800-59402000	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr1:59398800-59403000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:59399000-59399400	Enhancers	Colon Smooth Muscle	Colon
50	chr1:59399000-59399600	Enhancers	NH-A	brain

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