Variant report

Variant	rs12097260
Chromosome Location	chr1:169317195-169317196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169317063..169319375-chr1:169454243..169457078,2	K562	blood:
2	chr1:168604062..168606034-chr1:169316647..169318325,2	MCF-7	breast:
3	chr1:169315275..169317459-chr1:169319904..169321487,2	K562	blood:
4	chr1:169315565..169317290-chr1:169336784..169338618,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117475	Chromatin interaction
ENSG00000213062	Chromatin interaction
ENSG00000117479	Chromatin interaction
ENSG00000143156	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10047168	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10800430	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10800436	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10800443	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs10800445	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10919079	0.82[EUR][1000 genomes]
rs10919097	0.82[EUR][1000 genomes]
rs10919098	0.82[EUR][1000 genomes]
rs10919100	0.82[EUR][1000 genomes]
rs10919104	0.82[EUR][1000 genomes]
rs10919111	0.82[EUR][1000 genomes]
rs10919131	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10919151	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919152	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10919156	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919157	1.00[EUR][1000 genomes]
rs10919159	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11487548	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11802239	0.82[EUR][1000 genomes]
rs11805562	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11807896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11810815	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12058325	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12061069	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12061080	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12061405	0.82[EUR][1000 genomes]
rs12063056	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12063719	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12063863	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12065030	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12067139	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12067351	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12070031	0.82[EUR][1000 genomes]
rs12073439	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12074013	0.82[EUR][1000 genomes]
rs12074966	0.82[AFR][1000 genomes]
rs12076519	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12081030	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12081562	0.82[EUR][1000 genomes]
rs12082748	0.82[EUR][1000 genomes]
rs12083249	0.82[EUR][1000 genomes]
rs12088672	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12091133	0.91[EUR][1000 genomes]
rs12092506	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12092952	0.91[EUR][1000 genomes]
rs12094791	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12097682	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12561922	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12565852	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2275300	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2280257	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs3753298	0.82[EUR][1000 genomes]
rs3766052	0.82[EUR][1000 genomes]
rs3766064	0.82[EUR][1000 genomes]
rs3766082	0.82[EUR][1000 genomes]
rs3766088	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3766092	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3820057	0.82[EUR][1000 genomes]
rs41272453	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs57776592	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60011235	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61806984	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7515326	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544446	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9628661	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
2	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:169296600-169324600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:169303800-169317600	Weak transcription	Liver	Liver
5	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
6	chr1:169309200-169333600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:169309400-169336400	Weak transcription	Ovary	ovary
8	chr1:169310800-169332800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:169314800-169318200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:169316000-169334200	Weak transcription	Fetal Intestine Small	intestine
12	chr1:169316400-169321800	Weak transcription	HUVEC	blood vessel
13	chr1:169316600-169318000	Enhancers	Fetal Brain Male	brain
14	chr1:169316600-169318200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:169316800-169317200	Enhancers	Fetal Heart	heart
16	chr1:169317000-169317200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:169317000-169318000	Enhancers	Colon Smooth Muscle	Colon
18	chr1:169317000-169318000	Weak transcription	Fetal Intestine Large	intestine
19	chr1:169317000-169318200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:169317000-169318200	Enhancers	A549	lung
21	chr1:169317000-169336400	Weak transcription	Pancreas	Pancrea

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