Variant report

Variant	rs73175880
Chromosome Location	chr3:119723117-119723118
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119721357..119723738-chr3:119814057..119815870,3	MCF-7	breast:
2	chr3:119709355..119712243-chr3:119721755..119723709,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1054190	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11914561	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11915898	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11916594	0.95[EUR][1000 genomes]
rs11919783	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11923782	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11923854	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11927667	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1381841	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17204605	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17205095	0.95[EUR][1000 genomes]
rs17810302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55644728	0.83[AMR][1000 genomes]
rs55658250	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55910624	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs56114552	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6765004	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs68194015	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73175828	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73175830	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73175844	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73175849	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73175853	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73175858	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73175860	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73175862	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73175863	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73175864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175877	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175879	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73175886	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73175888	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175891	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73175897	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73177904	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73177905	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73177907	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7645180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119681200-119723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:119692400-119723200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr3:119693600-119732200	Weak transcription	A549	lung
4	chr3:119710200-119730800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:119711400-119729200	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:119711800-119723200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:119712000-119723400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:119712000-119732200	Weak transcription	HepG2	liver
9	chr3:119712200-119723400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:119712200-119732400	Weak transcription	NHLF	lung
11	chr3:119712600-119745000	Weak transcription	Hela-S3	cervix
12	chr3:119712800-119723400	Weak transcription	Osteobl	bone
13	chr3:119712800-119732200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:119713200-119744400	Weak transcription	Fetal Kidney	kidney
15	chr3:119717400-119730200	Weak transcription	Brain Anterior Caudate	brain
16	chr3:119717600-119732200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:119718200-119736800	Weak transcription	Liver	Liver
18	chr3:119719000-119729800	Weak transcription	Brain Substantia Nigra	brain
19	chr3:119719600-119723400	Weak transcription	NHEK	skin
20	chr3:119719600-119730000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:119720000-119723200	Weak transcription	Dnd41	blood
22	chr3:119720200-119731800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:119720200-119736600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:119720200-119741000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:119720400-119729600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:119720400-119730400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:119720400-119737200	Weak transcription	NHDF-Ad	bronchial
28	chr3:119720600-119723200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:119720800-119730200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:119720800-119738600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:119721000-119723200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:119721000-119724200	Weak transcription	Adipose Nuclei	Adipose
33	chr3:119721000-119724400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:119721000-119731200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:119721000-119731200	Weak transcription	Fetal Lung	lung
36	chr3:119721200-119723200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:119721400-119733600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:119722000-119723400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:119722600-119723200	Enhancers	Fetal Muscle Trunk	muscle
40	chr3:119722600-119723200	Enhancers	Pancreas	Pancrea
41	chr3:119722600-119723200	Enhancers	Psoas Muscle	Psoas
42	chr3:119722600-119723400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:119722600-119723400	Enhancers	Brain Angular Gyrus	brain
44	chr3:119722600-119723400	Enhancers	Esophagus	oesophagus
45	chr3:119722600-119723400	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr3:119722600-119723400	Flanking Active TSS	K562	blood
47	chr3:119722600-119723600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:119722600-119723600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:119722600-119723600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr3:119722600-119723600	Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links