Variant report

Variant	rs12633175
Chromosome Location	chr3:105585254-105585255
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105584001..105586223-chr3:105590379..105592467,2	MCF-7	breast:
2	chr3:105579577..105582453-chr3:105582537..105585477,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12630062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12633624	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1550713	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1972939	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2301031	1.00[AMR][1000 genomes]
rs2301033	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2301042	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34078396	0.92[EUR][1000 genomes]
rs3772534	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3862048	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55980746	1.00[AMR][1000 genomes];0.92[EUR][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	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1008564	chr3:105554580-105643435	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1008876	chr3:105554580-105645373	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877312	chr3:105560638-105916506	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
2	chr3:105557800-105586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:105558600-105586600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:105561600-105586200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:105562000-105586000	Weak transcription	K562	blood
6	chr3:105563000-105586800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:105568000-105586200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:105568000-105586200	Weak transcription	Pancreas	Pancrea
9	chr3:105568800-105586200	Weak transcription	Colonic Mucosa	Colon
10	chr3:105569800-105586200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:105572000-105586200	Weak transcription	Lung	lung
12	chr3:105572200-105585400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:105572600-105585800	Weak transcription	Fetal Thymus	thymus
14	chr3:105572800-105585800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:105579800-105585600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:105579800-105585800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:105581400-105585600	Weak transcription	Aorta	Aorta
18	chr3:105581800-105586200	Weak transcription	Gastric	stomach
19	chr3:105581800-105588800	Active TSS	Right Ventricle	heart
20	chr3:105582000-105585400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
21	chr3:105582200-105588200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:105582200-105589000	Active TSS	Right Atrium	heart
23	chr3:105582600-105585400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:105582800-105585600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:105582800-105585800	Transcr. at gene 5' and 3'	Osteobl	bone
26	chr3:105582800-105586200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:105583000-105585800	Enhancers	Fetal Intestine Small	intestine
28	chr3:105583200-105586200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:105583200-105586200	Enhancers	Hela-S3	cervix
30	chr3:105583200-105586800	Weak transcription	Spleen	Spleen
31	chr3:105583400-105585600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:105583400-105586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:105583600-105585600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:105583600-105589000	Active TSS	Left Ventricle	heart
35	chr3:105583800-105585600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr3:105584000-105585800	Enhancers	Brain Anterior Caudate	brain
37	chr3:105584000-105586200	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
38	chr3:105584200-105585400	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
39	chr3:105584200-105585400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr3:105584200-105585400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:105584200-105585600	Enhancers	Colon Smooth Muscle	Colon
42	chr3:105584200-105585800	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr3:105584200-105585800	Enhancers	Brain Cingulate Gyrus	brain
44	chr3:105584200-105585800	Enhancers	Fetal Intestine Large	intestine
45	chr3:105584200-105586600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:105584200-105589200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:105584400-105585400	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:105584400-105586200	Enhancers	Brain Angular Gyrus	brain
49	chr3:105584400-105588600	Active TSS	HSMM	muscle
50	chr3:105584600-105585400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links