Variant report

Variant	rs9875489
Chromosome Location	chr3:142522855-142522856
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142442488..142444417-chr3:142520460..142522860,2	MCF-7	breast:
2	chr3:142294703..142296575-chr3:142522509..142525334,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144935	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10049098	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10049364	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10935469	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12330897	0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs12330901	1.00[AMR][1000 genomes]
rs13320613	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13322816	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13325615	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13434361	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16834067	1.00[AMR][1000 genomes]
rs16852648	1.00[AMR][1000 genomes]
rs16852649	1.00[AMR][1000 genomes]
rs16852658	1.00[AMR][1000 genomes]
rs1916641	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs28373594	1.00[AMR][1000 genomes]
rs28460347	1.00[AMR][1000 genomes]
rs28505293	1.00[AMR][1000 genomes]
rs28564963	1.00[AMR][1000 genomes]
rs28572271	1.00[AMR][1000 genomes]
rs28678273	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28728040	1.00[AMR][1000 genomes]
rs58015805	1.00[AMR][1000 genomes]
rs6798447	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs72988606	1.00[AMR][1000 genomes]
rs72988611	1.00[AMR][1000 genomes]
rs72988625	1.00[AMR][1000 genomes]
rs72990716	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72992624	1.00[AMR][1000 genomes]
rs72992644	1.00[AMR][1000 genomes]
rs72992647	1.00[AMR][1000 genomes]
rs72992650	1.00[AMR][1000 genomes]
rs73002086	1.00[AMR][1000 genomes]
rs73002087	1.00[AMR][1000 genomes]
rs7622773	1.00[AMR][1000 genomes]
rs7637053	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7641418	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9289650	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9809475	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9810360	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9810606	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9811051	0.84[AFR][1000 genomes]
rs9819681	1.00[AMR][1000 genomes]
rs9823492	0.94[YRI][hapmap]
rs9826191	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9827373	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9836232	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9837730	0.94[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9839771	1.00[AMR][1000 genomes]
rs9846572	1.00[AMR][1000 genomes]
rs9847616	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9850432	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9863330	1.00[AMR][1000 genomes]
rs9867286	1.00[AMR][1000 genomes]
rs9867886	1.00[AMR][1000 genomes]
rs9877174	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9877670	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9879367	1.00[AMR][1000 genomes]
rs9882985	0.93[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	nsv1000631	chr3:142516367-142572058	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142468200-142525200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:142468400-142525200	Weak transcription	Fetal Brain Male	brain
3	chr3:142468400-142526800	Weak transcription	NHDF-Ad	bronchial
4	chr3:142468400-142529400	Weak transcription	Brain Germinal Matrix	brain
5	chr3:142468600-142525200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:142475000-142527200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:142488800-142527000	Weak transcription	Brain Anterior Caudate	brain
8	chr3:142490200-142529400	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:142495400-142527000	Weak transcription	Brain Angular Gyrus	brain
10	chr3:142498600-142526800	Weak transcription	Osteobl	bone
11	chr3:142499000-142527000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:142499400-142547800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:142501600-142525000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:142501600-142525600	Weak transcription	Fetal Stomach	stomach
15	chr3:142501800-142527000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:142501800-142528000	Weak transcription	Left Ventricle	heart
17	chr3:142501800-142535600	Weak transcription	Aorta	Aorta
18	chr3:142502000-142529400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:142504200-142523200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:142510400-142527200	Weak transcription	A549	lung
21	chr3:142510600-142523600	Weak transcription	HepG2	liver
22	chr3:142513600-142523400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:142513600-142527200	Weak transcription	Brain Substantia Nigra	brain
24	chr3:142513800-142523200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:142514600-142523400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:142514800-142572000	Weak transcription	Right Ventricle	heart
27	chr3:142515000-142523400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:142515000-142530800	Weak transcription	HSMM	muscle
29	chr3:142515600-142527000	Weak transcription	K562	blood
30	chr3:142517600-142526800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:142517800-142523200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:142518800-142527200	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:142519000-142572000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:142519200-142523400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:142519200-142526600	Weak transcription	NHLF	lung
36	chr3:142519800-142530000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:142520800-142525000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr3:142521000-142523200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:142521200-142523200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:142521400-142523000	Strong transcription	Ovary	ovary
41	chr3:142521400-142525000	Strong transcription	Adipose Nuclei	Adipose
42	chr3:142521400-142525200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:142521400-142528800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:142521600-142523200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:142521600-142526800	Weak transcription	NH-A	brain
46	chr3:142522000-142523000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:142522200-142526600	Weak transcription	Fetal Lung	lung
48	chr3:142522200-142526800	Weak transcription	HMEC	breast
49	chr3:142522200-142551800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:142522400-142530000	Weak transcription	H9 Cell Line	embryonic stem cell

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