Variant report

Variant	rs4259003
Chromosome Location	chr3:142523555-142523556
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142517462..142521813-chr3:142523317..142528126,6	K562	blood:
2	chr3:142522907..142524681-chr3:142538977..142541173,2	MCF-7	breast:
3	chr3:142294703..142296575-chr3:142522509..142525334,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251787	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1132030	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11715459	0.94[CHB][hapmap]
rs11717993	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1382688	0.85[CEU][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2033912	0.87[CEU][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2049328	0.87[CEU][hapmap];0.88[CHB][hapmap]
rs2140433	0.85[CEU][hapmap]
rs2177397	0.85[CEU][hapmap]
rs2177398	0.87[CEU][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2354856	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28524951	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28658009	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28689551	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34445140	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3821647	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3844273	0.89[MEX][hapmap];0.81[TSI][hapmap]
rs4398471	0.85[CEU][hapmap]
rs45497994	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4643748	0.86[CEU][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55722370	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56666685	0.86[EUR][1000 genomes]
rs57026466	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59108985	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60294656	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60319320	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60752859	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6440096	0.85[CEU][hapmap]
rs6440104	0.88[CHB][hapmap]
rs6440108	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6440110	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66897945	0.84[EUR][1000 genomes]
rs6772222	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6773213	0.85[CEU][hapmap]
rs6777466	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6797745	0.85[CEU][hapmap]
rs6798849	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6800573	0.85[CEU][hapmap]
rs6803681	0.87[CEU][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6807862	0.80[EUR][1000 genomes]
rs73232711	0.86[EUR][1000 genomes]
rs7621642	0.87[CEU][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7622662	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7623762	0.88[CHB][hapmap]
rs7623977	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7631245	0.82[CHB][hapmap];0.83[MEX][hapmap]
rs7637846	0.87[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7638338	0.85[CEU][hapmap]
rs7638459	0.87[CEU][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7639403	0.87[CEU][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7641514	0.87[CEU][hapmap];0.88[CHB][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs7642332	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7646197	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7653309	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7772	0.83[TSI][hapmap]
rs936339	0.95[EUR][1000 genomes]
rs953239	0.94[CHB][hapmap]
rs953641	0.87[CEU][hapmap];0.88[CHB][hapmap];0.91[TSI][hapmap]
rs9758429	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9815607	0.88[ASW][hapmap];0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9824476	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9835135	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9836269	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9849461	0.87[CEU][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9851381	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9857567	0.85[CEU][hapmap]
rs9862686	0.85[CEU][hapmap]
rs9864230	0.87[CEU][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9868309	0.85[CEU][hapmap]
rs9868886	0.87[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv820119	chr3:142523218-142525209	Strong transcription Weak transcription Enhancers	Chromatin interactive region	1 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	chr3:142510400-142527200	Weak transcription	A549	lung
20	chr3:142510600-142523600	Weak transcription	HepG2	liver
21	chr3:142513600-142527200	Weak transcription	Brain Substantia Nigra	brain
22	chr3:142514800-142572000	Weak transcription	Right Ventricle	heart
23	chr3:142515000-142530800	Weak transcription	HSMM	muscle
24	chr3:142515600-142527000	Weak transcription	K562	blood
25	chr3:142517600-142526800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:142518800-142527200	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:142519000-142572000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:142519200-142526600	Weak transcription	NHLF	lung
29	chr3:142519800-142530000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:142520800-142525000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr3:142521400-142525000	Strong transcription	Adipose Nuclei	Adipose
32	chr3:142521400-142525200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:142521400-142528800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:142521600-142526800	Weak transcription	NH-A	brain
35	chr3:142522200-142526600	Weak transcription	Fetal Lung	lung
36	chr3:142522200-142526800	Weak transcription	HMEC	breast
37	chr3:142522200-142551800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:142522400-142530000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:142522800-142523600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:142522800-142523600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:142522800-142524000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:142522800-142525000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:142522800-142528600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:142523000-142524600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:142523000-142525200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:142523000-142528200	Weak transcription	Ovary	ovary
47	chr3:142523200-142523800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:142523200-142524000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:142523200-142524800	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:142523200-142525000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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