Variant report

Variant	rs4682665
Chromosome Location	chr3:133919953-133919954
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	chr3:133919631..133921900-chr3:133925545..133928162,2	MCF-7	breast:
2	chr3:133916703..133918590-chr3:133919262..133920923,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163785	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12493731	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs28648514	0.81[EUR][1000 genomes]
rs4234422	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234423	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234424	0.95[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234426	0.95[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241371	1.00[JPT][hapmap]
rs4408870	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4447762	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4470517	0.95[CEU][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577436	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs4634087	0.81[CEU][hapmap]
rs4682655	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682656	0.82[EUR][1000 genomes]
rs4682657	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4682672	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4854617	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854618	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854619	0.95[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854813	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55688777	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56104814	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56205980	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62271183	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439459	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439467	0.92[EUR][1000 genomes]
rs6439470	0.86[CEU][hapmap];0.92[TSI][hapmap]
rs6439471	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6764932	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779423	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6783989	0.87[EUR][1000 genomes]
rs6787345	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6791361	0.81[EUR][1000 genomes]
rs6795532	0.95[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795658	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799962	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71807032	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7431604	0.94[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433368	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611104	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616326	0.81[EUR][1000 genomes]
rs7627059	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631521	0.90[EUR][1000 genomes]
rs7633386	0.94[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634265	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289461	0.95[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812346	0.95[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843401	0.95[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862959	1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870797	0.81[CEU][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs9883217	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs9884008	0.82[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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133874400-133929400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:133874600-133933600	Weak transcription	Colonic Mucosa	Colon
3	chr3:133877600-133935200	Weak transcription	Psoas Muscle	Psoas
4	chr3:133877800-133920200	Weak transcription	Brain Substantia Nigra	brain
5	chr3:133877800-133950200	Weak transcription	Small Intestine	intestine
6	chr3:133888400-133923600	Weak transcription	Fetal Heart	heart
7	chr3:133894800-133935200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:133894800-133946800	Weak transcription	Pancreas	Pancrea
9	chr3:133895000-133950000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:133895000-133950200	Weak transcription	Gastric	stomach
11	chr3:133895200-133927200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:133895600-133942800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:133895800-133923400	Weak transcription	Lung	lung
14	chr3:133902000-133930400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:133903000-133929000	Weak transcription	GM12878-XiMat	blood
16	chr3:133907800-133927400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:133909200-133920400	Weak transcription	Brain Angular Gyrus	brain
18	chr3:133909200-133943000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:133911600-133929600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:133911600-133929800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:133916200-133920200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:133917200-133920400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:133917400-133921600	Strong transcription	Stomach Smooth Muscle	stomach
24	chr3:133917400-133921800	Strong transcription	Liver	Liver
25	chr3:133917400-133921800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr3:133917400-133922000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:133917400-133922400	Strong transcription	Primary B cells from cord blood	blood
28	chr3:133917800-133920800	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:133917800-133920800	Strong transcription	Thymus	Thymus
30	chr3:133917800-133921200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:133917800-133921200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:133917800-133921400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr3:133917800-133921600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:133917800-133921600	Strong transcription	Fetal Muscle Leg	muscle
35	chr3:133917800-133921600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:133917800-133921800	Strong transcription	Primary T cells from cord blood	blood
37	chr3:133917800-133921800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr3:133917800-133922000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:133917800-133922200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:133917800-133922200	Strong transcription	Adipose Nuclei	Adipose
41	chr3:133917800-133922800	Strong transcription	Fetal Thymus	thymus
42	chr3:133917800-133925000	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:133918000-133920000	Strong transcription	Fetal Intestine Small	intestine
44	chr3:133918000-133920200	Strong transcription	Brain Hippocampus Middle	brain
45	chr3:133918000-133920400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:133918000-133920800	Strong transcription	Ovary	ovary
47	chr3:133918000-133920800	Strong transcription	Spleen	Spleen
48	chr3:133918000-133921200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:133918000-133921200	Strong transcription	Left Ventricle	heart
50	chr3:133918000-133921200	Strong transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links