Variant report

Variant	rs11919783
Chromosome Location	chr3:119746633-119746634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119743278..119746755-chr3:119748847..119751492,3	MCF-7	breast:
2	chr3:119745451..119747987-chr3:119811711..119814390,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	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]
rs11914561	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11915898	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11916594	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11923782	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11923854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11927667	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1381841	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17204605	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17205095	0.94[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17810302	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17811013	0.90[GIH][hapmap]
rs55658250	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55910624	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56114552	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6765004	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs68194015	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73175828	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73175830	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73175844	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73175849	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73175853	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73175858	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73175860	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73175862	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73175863	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73175864	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73175870	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73175873	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73175877	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73175879	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175880	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175886	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73175891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175897	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73177904	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73177905	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73177907	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7645180	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[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:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119731400-119752400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:119732200-119747200	Weak transcription	Gastric	stomach
3	chr3:119732200-119747600	Weak transcription	Right Ventricle	heart
4	chr3:119732600-119748400	Weak transcription	Brain Angular Gyrus	brain
5	chr3:119732600-119748600	Weak transcription	HSMM	muscle
6	chr3:119732600-119757800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:119732800-119749200	Weak transcription	Fetal Stomach	stomach
8	chr3:119733000-119747400	Weak transcription	Right Atrium	heart
9	chr3:119734800-119750000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:119735000-119751600	Weak transcription	Primary B cells from cord blood	blood
11	chr3:119737000-119749400	Weak transcription	Stomach Mucosa	stomach
12	chr3:119737000-119751800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr3:119737400-119751800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:119737400-119754000	Weak transcription	Small Intestine	intestine
15	chr3:119737800-119757200	Weak transcription	A549	lung
16	chr3:119738400-119747000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:119738600-119747000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:119739400-119756000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:119739600-119749400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:119740000-119747000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:119740000-119747200	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:119740000-119747400	Weak transcription	Lung	lung
23	chr3:119740000-119747400	Weak transcription	Ovary	ovary
24	chr3:119740000-119747600	Weak transcription	Pancreas	Pancrea
25	chr3:119740000-119758200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:119740600-119748400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:119740800-119753400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:119741000-119758000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:119741200-119748400	Weak transcription	HSMMtube	muscle
30	chr3:119741200-119758400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:119741600-119749000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:119741800-119747400	Weak transcription	Left Ventricle	heart
33	chr3:119741800-119747400	Weak transcription	Psoas Muscle	Psoas
34	chr3:119741800-119747600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:119741800-119753600	Weak transcription	Thymus	Thymus
36	chr3:119742000-119747000	Weak transcription	Brain Substantia Nigra	brain
37	chr3:119742000-119747000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:119742000-119748400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:119742000-119754400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:119742000-119758000	Weak transcription	NHDF-Ad	bronchial
41	chr3:119742200-119746800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:119742200-119747200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:119742400-119747600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:119742600-119747200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:119742600-119752200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:119742600-119757000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:119742800-119747200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:119743200-119747600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:119743800-119747000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:119744200-119747600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links