Variant report

Variant	rs62335341
Chromosome Location	chr4:158930564-158930565
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:158924817..158927091-chr4:158928943..158930898,2	MCF-7	breast:
2	chr4:158929309..158930813-chr4:159080640..159082644,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164125	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10517684	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10857307	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10857308	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11100145	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12498860	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12501025	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12504989	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12505752	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12505934	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12510436	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12511544	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12511578	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12511957	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12512064	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12643255	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12644342	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12650454	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1375138	0.82[EUR][1000 genomes]
rs17036918	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17036921	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1839129	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1839130	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2594763	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2594769	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35146306	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35354204	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3934848	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4077777	0.84[ASN][1000 genomes]
rs4129400	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4132016	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4132443	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4307005	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4460050	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4464607	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4629502	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4637451	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4691449	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57156989	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58762368	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62335304	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62335305	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62335306	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62335307	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62335308	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62335310	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62335311	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62335313	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62335314	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62335315	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62335316	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62335317	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62335339	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62335345	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62335346	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62335358	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62335359	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62336960	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62336961	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62336984	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6815131	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827475	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72965897	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72967808	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72967836	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964237	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs982239	0.94[AMR][1000 genomes];0.95[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	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv881288	chr4:158891733-159028080	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:158923800-158939400	Weak transcription	HepG2	liver
2	chr4:158925600-158930600	Enhancers	Colon Smooth Muscle	Colon
3	chr4:158926000-158938800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:158926600-158931000	Enhancers	HUVEC	blood vessel
5	chr4:158927600-158933600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:158928000-158933200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:158928400-158930600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:158928400-158936200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:158928800-158930600	Enhancers	NH-A	brain
10	chr4:158928800-158932600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr4:158929800-158930600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:158929800-158930600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:158929800-158930600	Enhancers	Left Ventricle	heart
14	chr4:158929800-158931000	Enhancers	Fetal Muscle Leg	muscle
15	chr4:158929800-158931000	Enhancers	HMEC	breast
16	chr4:158929800-158933000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:158929800-158933000	Enhancers	Ovary	ovary
18	chr4:158930000-158930600	Enhancers	NHEK	skin
19	chr4:158930000-158930800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:158930000-158932600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr4:158930200-158933000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr4:158930200-158934600	Weak transcription	HSMM	muscle
23	chr4:158930200-158934600	Weak transcription	Osteobl	bone
24	chr4:158930200-158937400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:158930200-158940800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:158930400-158930600	Enhancers	Brain Substantia Nigra	brain
27	chr4:158930400-158930800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:158930400-158931200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:158930400-158931600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:158930400-158932600	Weak transcription	Right Atrium	heart
31	chr4:158930400-158934400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr4:158930400-158934400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:158930400-158934600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:158930400-158935400	Weak transcription	Brain Anterior Caudate	brain
35	chr4:158930400-158936000	Weak transcription	HSMMtube	muscle
36	chr4:158930400-158940800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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