Variant report

Variant	rs28698461
Chromosome Location	chr12:123881928-123881929
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123879767..123882314-chr12:123882742..123884960,2	MCF-7	breast:
2	chr12:123873357..123876856-chr12:123879238..123882589,5	K562	blood:
3	chr12:123881385..123883627-chr12:123929394..123932361,2	MCF-7	breast:
4	chr12:123881479..123883562-chr12:123887318..123890802,3	MCF-7	breast:
5	chr12:123880916..123883261-chr12:123885627..123887999,2	K562	blood:

Variant related genes	Relation type
ENSG00000183955	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10846516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11057239	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11057252	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs11057257	1.00[AMR][1000 genomes]
rs11057265	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11057272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11057278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11057281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11057282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2280424	1.00[YRI][hapmap]
rs28553365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28624763	0.88[EUR][1000 genomes]
rs28664930	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs28690392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28828722	0.94[EUR][1000 genomes]
rs28836481	0.85[EUR][1000 genomes]
rs28875264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3759111	1.00[YRI][hapmap]
rs3759114	1.00[YRI][hapmap]
rs3881293	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4759407	1.00[YRI][hapmap]
rs4759408	1.00[YRI][hapmap]
rs4759411	1.00[YRI][hapmap]
rs4759413	1.00[YRI][hapmap]
rs4759414	1.00[YRI][hapmap]
rs55634633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55932027	1.00[EUR][1000 genomes]
rs73216930	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73216932	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73231994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73233508	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7486351	1.00[AMR][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

No data

Chromatin state (count:127 , 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	chr12:123875400-123882200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:123875400-123882600	Strong transcription	Placenta	Placenta
8	chr12:123875400-123883600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:123875400-123884600	Strong transcription	Primary T cells from cord blood	blood
10	chr12:123875600-123882200	Strong transcription	Colon Smooth Muscle	Colon
11	chr12:123875600-123882800	Weak transcription	Psoas Muscle	Psoas
12	chr12:123875600-123884000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:123875600-123884200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:123875600-123884200	Strong transcription	A549	lung
15	chr12:123875600-123884200	Strong transcription	GM12878-XiMat	blood
16	chr12:123875600-123884400	Strong transcription	HMEC	breast
17	chr12:123875600-123884600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:123875600-123885400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:123875600-123894200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:123875600-123895600	Strong transcription	Fetal Thymus	thymus
21	chr12:123875800-123882000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:123875800-123882200	Strong transcription	NHEK	skin
23	chr12:123875800-123884200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr12:123875800-123884600	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr12:123875800-123894000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:123876000-123884400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr12:123876200-123882800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:123876200-123884400	Strong transcription	Fetal Lung	lung
29	chr12:123876200-123885600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:123876400-123882600	Strong transcription	Liver	Liver
31	chr12:123876400-123884600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:123876400-123894800	Strong transcription	Fetal Intestine Small	intestine
33	chr12:123876600-123882000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:123876600-123882000	Strong transcription	HSMMtube	muscle
35	chr12:123876600-123884000	Strong transcription	Duodenum Mucosa	Duodenum
36	chr12:123876600-123894800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:123876800-123882200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:123876800-123882400	Strong transcription	Hela-S3	cervix
39	chr12:123876800-123882600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:123876800-123882800	Strong transcription	Adipose Nuclei	Adipose
41	chr12:123876800-123882800	Weak transcription	Right Atrium	heart
42	chr12:123876800-123884200	Strong transcription	K562	blood
43	chr12:123876800-123884400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:123876800-123884400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:123876800-123885400	Strong transcription	Fetal Brain Female	brain
46	chr12:123876800-123887600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr12:123877000-123885000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:123877000-123885600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:123877200-123884400	Strong transcription	Brain Germinal Matrix	brain
50	chr12:123877400-123882800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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