Variant report

Variant	rs1060569
Chromosome Location	chr3:119236887-119236888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119216267..119219022-chr3:119234970..119238819,4	MCF-7	breast:
2	chr3:119231563..119234574-chr3:119234818..119238744,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272662	Chromatin interaction
ENSG00000113845	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10934493	0.80[AFR][1000 genomes]
rs13080905	0.94[ASN][1000 genomes]
rs1797839	0.91[ASN][1000 genomes]
rs1900742	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1919586	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1919590	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1967621	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976919	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030816	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2177812	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732413	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3814397	0.91[ASN][1000 genomes]
rs4687855	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4687860	0.94[ASN][1000 genomes]
rs4688005	0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4688007	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4688008	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688012	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688014	0.89[ASN][1000 genomes]
rs6414282	0.91[ASN][1000 genomes]
rs6414283	0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6438528	0.94[ASN][1000 genomes]
rs6438529	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6438530	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6438531	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6438535	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777535	0.94[ASN][1000 genomes]
rs6778945	0.92[ASN][1000 genomes]
rs6794822	0.91[ASN][1000 genomes]
rs6796970	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs727905	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73189804	0.82[AFR][1000 genomes]
rs73189805	0.80[AFR][1000 genomes]
rs7430798	0.94[ASN][1000 genomes]
rs7621259	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628626	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630587	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7642502	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289129	0.94[ASN][1000 genomes]
rs9809155	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9836326	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9836627	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850447	0.92[ASN][1000 genomes]
rs9867768	0.92[ASN][1000 genomes]
rs9873196	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874480	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9877854	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119219600-119237000	Weak transcription	Small Intestine	intestine
2	chr3:119219800-119239200	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:119220000-119243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:119220200-119246800	Weak transcription	Stomach Mucosa	stomach
5	chr3:119220800-119243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:119221000-119244600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:119221200-119243600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:119221200-119244400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:119221400-119245400	Strong transcription	Placenta	Placenta
10	chr3:119221600-119237400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:119221600-119244600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:119222000-119245400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:119224000-119245200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:119226000-119245200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:119226000-119245200	Strong transcription	Liver	Liver
16	chr3:119226600-119245200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:119227000-119239800	Weak transcription	Psoas Muscle	Psoas
18	chr3:119227400-119245400	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:119228000-119243600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:119228000-119250000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:119229200-119240200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:119229200-119244600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:119229400-119237000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:119230600-119245400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr3:119230800-119244400	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr3:119231200-119237800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:119231200-119237800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:119231200-119244000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:119231600-119238200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:119231600-119238200	Strong transcription	NHLF	lung
31	chr3:119231600-119240000	Strong transcription	HSMM	muscle
32	chr3:119231600-119240000	Strong transcription	Osteobl	bone
33	chr3:119231600-119240600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:119231600-119243400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:119231800-119237400	Strong transcription	Fetal Lung	lung
36	chr3:119231800-119238200	Strong transcription	Brain Cingulate Gyrus	brain
37	chr3:119231800-119238800	Strong transcription	NHDF-Ad	bronchial
38	chr3:119231800-119239400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:119231800-119239400	Strong transcription	Primary B cells from cord blood	blood
40	chr3:119231800-119240200	Strong transcription	Primary T cells from cord blood	blood
41	chr3:119231800-119240200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:119231800-119240200	Strong transcription	Fetal Brain Male	brain
43	chr3:119231800-119240600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:119231800-119240800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:119231800-119243200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:119231800-119243400	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr3:119231800-119244000	Strong transcription	Adipose Nuclei	Adipose
48	chr3:119231800-119244800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:119231800-119245400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:119231800-119257200	Strong transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links