Variant report

Variant	rs12581154
Chromosome Location	chr12:104951556-104951557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104950099..104952735-chr12:104953962..104957251,3	MCF-7	breast:
2	chr12:104944520..104947051-chr12:104950465..104952770,2	MCF-7	breast:
3	chr11:62607631..62609142-chr12:104951287..104952807,2	K562	blood:
4	chr12:104944181..104946936-chr12:104950412..104953121,2	K562	blood:
5	chr12:104951287..104952971-chr20:62151399..62153219,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125534	Chromatin interaction
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11112103	1.00[EUR][1000 genomes]
rs12580732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12581196	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12581471	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12581482	1.00[ASW][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12581832	1.00[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12582770	0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12582786	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1625417	0.88[JPT][hapmap]
rs1704903	0.88[JPT][hapmap]
rs1704921	0.88[JPT][hapmap]
rs1704922	0.88[JPT][hapmap]
rs1795851	0.88[JPT][hapmap]
rs2665748	0.88[JPT][hapmap]
rs35340768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58027342	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58754129	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60941296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300706	0.90[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes]
rs7980620	0.90[CHB][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1035364	chr12:104948307-105003705	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104930200-104957600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:104940600-104958000	Weak transcription	K562	blood
3	chr12:104941400-104959400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:104942000-104957600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:104944400-104957600	Weak transcription	A549	lung
6	chr12:104944800-104951600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr12:104947400-104958000	Weak transcription	Primary T cells from cord blood	blood
8	chr12:104947600-104952800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:104947800-104954600	Weak transcription	Primary B cells from cord blood	blood
10	chr12:104947800-104961200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:104947800-104964400	Weak transcription	Aorta	Aorta
12	chr12:104948000-104952600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:104948000-104954200	Weak transcription	GM12878-XiMat	blood
14	chr12:104948000-104957600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr12:104948200-104951600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:104948200-104954800	Weak transcription	Spleen	Spleen
17	chr12:104949000-104959400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:104949000-104960400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:104949000-104961400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:104949400-104957200	Strong transcription	Dnd41	blood
21	chr12:104949600-104957800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr12:104949600-104968800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:104949800-104951600	Weak transcription	Fetal Thymus	thymus
24	chr12:104949800-104951800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:104949800-104954400	Weak transcription	Right Ventricle	heart
26	chr12:104949800-104957800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr12:104949800-104957800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:104949800-104963400	Weak transcription	Lung	lung
29	chr12:104950000-104953200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:104950000-104957600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:104950000-104958000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:104950000-104978800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:104950200-104952000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:104950200-104958000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:104950200-104959200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:104950800-104951800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:104950800-104952000	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr12:104951000-104951600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr12:104951000-104951600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:104951000-104951600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:104951000-104951800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:104951000-104952000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr12:104951200-104951600	Enhancers	Brain Anterior Caudate	brain
44	chr12:104951200-104951800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:104951200-104951800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:104951400-104952200	Strong transcription	Thymus	Thymus
47	chr12:104951400-104952800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links