Variant report

Variant	rs12095486
Chromosome Location	chr1:180865555-180865556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180863020..180866201-chr1:180866515..180869291,3	MCF-7	breast:
2	chr1:180849863..180851365-chr1:180863238..180865700,2	MCF-7	breast:
3	chr1:180863449..180866060-chr1:180874584..180876590,2	MCF-7	breast:
4	chr1:180856327..180857845-chr1:180863830..180866237,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143324	Chromatin interaction
ENSG00000225857	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10914072	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs10914085	0.81[YRI][hapmap]
rs10914087	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs10914093	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs10914106	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs10914119	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs10914125	0.87[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12067934	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs12068624	0.81[YRI][hapmap]
rs12070064	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs12071498	0.85[YRI][hapmap]
rs12075235	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs12075809	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs12078050	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs12080611	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs12081764	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs12086559	0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12088182	0.87[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs12088430	0.82[MKK][hapmap]
rs12088485	1.00[MEX][hapmap];0.84[MKK][hapmap]
rs12089778	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091686	0.81[YRI][hapmap]
rs12092161	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs12092920	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12096475	0.87[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58065433	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59562665	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6425654	1.00[MEX][hapmap]
rs6659121	0.81[YRI][hapmap]
rs6672886	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs6676373	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6686881	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs6691204	0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6692456	1.00[MEX][hapmap]
rs6693045	1.00[MEX][hapmap];0.85[MKK][hapmap]
rs73047730	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73047732	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73047734	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73047747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73047748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7528848	1.00[MEX][hapmap]
rs7542521	1.00[MEX][hapmap];0.82[MKK][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180805800-180881000	Weak transcription	Aorta	Aorta
2	chr1:180812200-180867000	Weak transcription	Ovary	ovary
3	chr1:180824000-180867600	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:180824000-180880800	Weak transcription	Right Ventricle	heart
5	chr1:180828600-180867800	Weak transcription	HSMM	muscle
6	chr1:180830000-180867600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:180835800-180870400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:180841000-180867800	Weak transcription	Lung	lung
9	chr1:180844200-180872200	Weak transcription	Esophagus	oesophagus
10	chr1:180844400-180867400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:180845800-180869000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:180847400-180875400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:180849400-180867200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:180851000-180867000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:180851400-180867400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:180851400-180867600	Weak transcription	Fetal Heart	heart
17	chr1:180851600-180867600	Weak transcription	Brain Germinal Matrix	brain
18	chr1:180851600-180867800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:180851800-180867400	Weak transcription	Fetal Intestine Small	intestine
20	chr1:180852000-180870400	Weak transcription	A549	lung
21	chr1:180853600-180867200	Weak transcription	Adipose Nuclei	Adipose
22	chr1:180853800-180867800	Weak transcription	Fetal Stomach	stomach
23	chr1:180854000-180866400	Weak transcription	Primary B cells from cord blood	blood
24	chr1:180854400-180866800	Weak transcription	Left Ventricle	heart
25	chr1:180854800-180866800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:180857200-180867400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:180857600-180869600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:180858400-180870600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:180858800-180867400	Weak transcription	Fetal Brain Female	brain
30	chr1:180861200-180880800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:180862200-180867400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:180863200-180867000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr1:180863400-180867400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:180863600-180866600	Weak transcription	Primary T cells from cord blood	blood
35	chr1:180863600-180868000	Weak transcription	Fetal Thymus	thymus
36	chr1:180863600-180868000	Weak transcription	Right Atrium	heart
37	chr1:180864600-180870200	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links