Variant report

Variant	rs13091979
Chromosome Location	chr3:45980110-45980111
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:45979960-45980110	GM12866	blood:	n/a	n/a
2	RAD21	chr3:45980057-45980899	SK-N-SH	brain:	n/a	chr3:45980442-45980455 chr3:45980441-45980448 chr3:45980443-45980452 chr3:45980439-45980458
3	SMC3	chr3:45980050-45981293	SK-N-SH	brain:	n/a	chr3:45980440-45980454
4	CTCF	chr3:45980030-45980917	A549	lung:	n/a	chr3:45980439-45980455 chr3:45980441-45980454 chr3:45980438-45980456 chr3:45980443-45980451 chr3:45980440-45980461

No.	Distal block	Cell Line	Cell type
1	chr3:45979895..45980974-chr3:46119979..46120805,8	MCF-7	breast:
2	chr3:45980083..45981150-chr3:46117757..46119043,6	MCF-7	breast:
3	chr3:45979997..45980877-chr3:46419945..46420540,2	K562	blood:
4	chr3:45979945..45981160-chr3:46119722..46121315,21	K562	blood:
5	chr3:45978760..45981889-chr3:46119716..46121321,25	MCF-7	breast:
6	chr3:45979978..45982491-chr3:46035904..46038054,2	MCF-7	breast:
7	chr3:45980001..45980840-chr3:46121974..46122633,2	K562	blood:
8	chr3:45978904..45980774-chr3:45983050..45984937,2	MCF-7	breast:
9	chr3:45979673..45982315-chr3:46020948..46022553,2	K562	blood:

Variant related genes	Relation type
CXCR6	TF binding region
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1072755	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130080	0.80[EUR][1000 genomes]
rs12630101	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12635494	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12639598	0.80[EUR][1000 genomes]
rs13066048	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13091821	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532071	0.91[ASN][1000 genomes]
rs1552489	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1552490	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1601867	0.89[ASN][1000 genomes]
rs1994488	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1994489	0.91[ASN][1000 genomes]
rs2054866	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2171530	0.82[ASN][1000 genomes]
rs2234358	0.88[ASN][1000 genomes]
rs2248228	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291470	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35465473	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3733103	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3774634	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3774635	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3774639	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3796373	0.82[ASN][1000 genomes]
rs3796375	0.80[EUR][1000 genomes]
rs4535265	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4682799	0.91[ASN][1000 genomes]
rs4682800	0.91[ASN][1000 genomes]
rs4683148	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4683149	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683152	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683154	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4683156	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4683157	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6778896	0.80[EUR][1000 genomes]
rs7129	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs751552	0.80[EUR][1000 genomes]
rs751553	0.80[EUR][1000 genomes]
rs9311380	0.91[ASN][1000 genomes]
rs936938	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9824253	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9831315	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 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	chr3:45958000-45980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:45958800-45980200	Strong transcription	Skeletal Muscle Male	skeletal muscle
3	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
4	chr3:45959200-45980400	Strong transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:45959800-45980400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:45960000-45980400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:45960400-45980200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:45963200-45985200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:45964400-45980400	Weak transcription	Fetal Brain Female	brain
11	chr3:45965400-45980400	Weak transcription	Fetal Brain Male	brain
12	chr3:45966000-45980600	Weak transcription	HMEC	breast
13	chr3:45968600-45980200	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr3:45970000-45980400	Weak transcription	Right Atrium	heart
15	chr3:45970200-45980400	Weak transcription	NH-A	brain
16	chr3:45970200-45980600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:45970200-45988200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:45971000-45980200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr3:45971400-45980200	Strong transcription	Dnd41	blood
20	chr3:45971800-45982400	Weak transcription	NHEK	skin
21	chr3:45972800-45988600	Weak transcription	Small Intestine	intestine
22	chr3:45973400-45986400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:45973600-45980600	Weak transcription	Brain Angular Gyrus	brain
24	chr3:45973800-45988000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:45973800-45991400	Weak transcription	Brain Germinal Matrix	brain
26	chr3:45974000-45980600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:45974400-45988000	Weak transcription	Fetal Kidney	kidney
28	chr3:45975400-45980600	Weak transcription	NHDF-Ad	bronchial
29	chr3:45976400-45980600	Strong transcription	Fetal Intestine Small	intestine
30	chr3:45976400-45981800	Strong transcription	Fetal Stomach	stomach
31	chr3:45976800-45980600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:45977000-45980600	Weak transcription	Psoas Muscle	Psoas
33	chr3:45977200-45980200	Strong transcription	Left Ventricle	heart
34	chr3:45977200-45980600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:45977400-45980400	Weak transcription	Fetal Heart	heart
36	chr3:45977400-45987000	Weak transcription	Fetal Lung	lung
37	chr3:45977400-45988000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:45977600-45983400	Weak transcription	Primary B cells from cord blood	blood
39	chr3:45977600-45987600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:45978000-45988000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:45978200-45980200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:45978200-45980400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr3:45978200-45980400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:45978200-45980400	Weak transcription	GM12878-XiMat	blood
45	chr3:45978200-45982200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:45978200-45988200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:45978400-45980200	Strong transcription	Right Ventricle	heart
48	chr3:45978400-45980400	Weak transcription	Osteobl	bone
49	chr3:45978400-45980600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:45978400-45983800	Weak transcription	Spleen	Spleen

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