Variant report

Variant	rs28540654
Chromosome Location	chr12:123882944-123882945
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123881385..123883627-chr12:123929394..123932361,2	MCF-7	breast:
2	chr12:123881479..123883562-chr12:123887318..123890802,3	MCF-7	breast:
3	chr12:123882533..123885309-chr12:123899138..123901801,2	MCF-7	breast:
4	chr12:123880916..123883261-chr12:123885627..123887999,2	K562	blood:
5	chr12:123879767..123882314-chr12:123882742..123884960,2	MCF-7	breast:
6	chr12:123847504..123849899-chr12:123882139..123884524,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139697	Chromatin interaction
ENSG00000256092	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11057298	1.00[JPT][hapmap]
rs11057302	1.00[JPT][hapmap]
rs12099981	1.00[JPT][hapmap]
rs1877365	1.00[JPT][hapmap]
rs28533432	0.96[YRI][hapmap]
rs28694725	1.00[JPT][hapmap]
rs61751328	1.00[EUR][1000 genomes]
rs6488866	1.00[EUR][1000 genomes]
rs7303355	1.00[EUR][1000 genomes]
rs7303554	1.00[JPT][hapmap]
rs7304190	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7958153	1.00[JPT][hapmap]
rs7962049	1.00[EUR][1000 genomes]
rs7971779	1.00[JPT][hapmap]
rs7980804	1.00[EUR][1000 genomes]
rs952360	1.00[JPT][hapmap]
rs9668616	1.00[EUR][1000 genomes]
rs9668827	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28540654	ABCB9	cis	lymphoblastoid	seeQTL
rs28540654	SETD8	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123875000-123884400	Strong transcription	Thymus	Thymus
2	chr12:123875000-123886400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:123875200-123884400	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr12:123875200-123884600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:123875200-123894400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:123875400-123883600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:123875400-123884600	Strong transcription	Primary T cells from cord blood	blood
8	chr12:123875600-123884000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:123875600-123884200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:123875600-123884200	Strong transcription	A549	lung
11	chr12:123875600-123884200	Strong transcription	GM12878-XiMat	blood
12	chr12:123875600-123884400	Strong transcription	HMEC	breast
13	chr12:123875600-123884600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:123875600-123885400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:123875600-123894200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:123875600-123895600	Strong transcription	Fetal Thymus	thymus
17	chr12:123875800-123884200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr12:123875800-123884600	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr12:123875800-123894000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:123876000-123884400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:123876200-123884400	Strong transcription	Fetal Lung	lung
22	chr12:123876200-123885600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:123876400-123884600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:123876400-123894800	Strong transcription	Fetal Intestine Small	intestine
25	chr12:123876600-123884000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr12:123876600-123894800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:123876800-123884200	Strong transcription	K562	blood
28	chr12:123876800-123884400	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr12:123876800-123884400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:123876800-123885400	Strong transcription	Fetal Brain Female	brain
31	chr12:123876800-123887600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:123877000-123885000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:123877000-123885600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:123877200-123884400	Strong transcription	Brain Germinal Matrix	brain
35	chr12:123877400-123884400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:123877400-123889000	Weak transcription	Fetal Heart	heart
37	chr12:123877400-123895600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:123877800-123884400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr12:123878000-123884000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr12:123878000-123884400	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr12:123878200-123884600	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:123879000-123883000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:123879000-123884200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:123879000-123884400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr12:123879000-123884600	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:123879600-123884600	Strong transcription	Dnd41	blood
47	chr12:123880600-123883000	Genic enhancers	Rectal Mucosa Donor 31	rectum
48	chr12:123880600-123883800	Genic enhancers	Gastric	stomach
49	chr12:123880600-123884200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:123881000-123883000	Genic enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links