Variant report

Variant	rs28694725
Chromosome Location	chr12:123893645-123893646
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123889075..123892344-chr12:123892398..123894933,4	K562	blood:
2	chr12:123892437..123894843-chr12:124070809..124073314,2	MCF-7	breast:
3	chr12:123889713..123892231-chr12:123892398..123893927,2	K562	blood:
4	chr12:123871220..123876084-chr12:123892723..123900288,8	K562	blood:

Variant related genes	Relation type
ENSG00000183955	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11057298	1.00[JPT][hapmap]
rs11057302	1.00[JPT][hapmap]
rs12099981	1.00[JPT][hapmap]
rs1877365	1.00[JPT][hapmap]
rs28540654	1.00[JPT][hapmap]
rs7303554	1.00[JPT][hapmap]
rs786428	1.00[JPT][hapmap]
rs786431	1.00[JPT][hapmap]
rs786439	1.00[JPT][hapmap]
rs7958153	1.00[JPT][hapmap]
rs7971779	1.00[JPT][hapmap]
rs952360	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription 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	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv975550	chr12:123888322-123893712	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv975551	chr12:123888322-123897046	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123875200-123894400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:123875600-123894200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:123875600-123895600	Strong transcription	Fetal Thymus	thymus
4	chr12:123875800-123894000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:123876400-123894800	Strong transcription	Fetal Intestine Small	intestine
6	chr12:123876600-123894800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:123877400-123895600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:123882000-123911600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:123883200-123895400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:123883800-123894200	Strong transcription	HUVEC	blood vessel
11	chr12:123883800-123895200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:123884200-123895200	Strong transcription	Fetal Muscle Trunk	muscle
13	chr12:123886000-123895200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:123886000-123895400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:123886200-123894200	Strong transcription	Fetal Intestine Large	intestine
16	chr12:123886200-123894800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:123886200-123895200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:123886200-123895200	Strong transcription	Fetal Muscle Leg	muscle
19	chr12:123886200-123895200	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:123886200-123895200	Strong transcription	Dnd41	blood
21	chr12:123886200-123895400	Strong transcription	Fetal Brain Female	brain
22	chr12:123886400-123894200	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:123886400-123894200	Strong transcription	Left Ventricle	heart
24	chr12:123886400-123894200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr12:123886400-123894400	Strong transcription	Osteobl	bone
26	chr12:123886400-123894800	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:123886400-123895000	Strong transcription	Adipose Nuclei	Adipose
28	chr12:123886400-123895000	Strong transcription	Liver	Liver
29	chr12:123886400-123895200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:123886400-123895200	Strong transcription	Spleen	Spleen
31	chr12:123886400-123895200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:123886400-123895200	Strong transcription	NHLF	lung
33	chr12:123886400-123895400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:123886400-123895400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:123886400-123895400	Strong transcription	Thymus	Thymus
36	chr12:123886600-123894000	Strong transcription	HSMMtube	muscle
37	chr12:123886600-123894200	Strong transcription	Primary B cells from peripheral blood	blood
38	chr12:123886600-123894200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr12:123886600-123894200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:123886600-123895000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:123886600-123895200	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:123886800-123894200	Strong transcription	Esophagus	oesophagus
43	chr12:123887000-123893800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:123887000-123894200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:123887000-123894200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:123887000-123895200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr12:123887000-123897600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr12:123887200-123893800	Strong transcription	Gastric	stomach
49	chr12:123887200-123894000	Strong transcription	Pancreas	Pancrea
50	chr12:123887200-123894400	Strong transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links