Variant report

Variant	rs12315409
Chromosome Location	chr12:67254942-67254943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:67253380..67256928-chr12:67258329..67261239,3	K562	blood:
2	chr12:67110006..67111455-chr12:67254721..67255586,6	MCF-7	breast:
3	chr12:67109764..67110463-chr12:67254735..67255402,2	MCF-7	breast:
4	chr12:67082410..67083294-chr12:67254648..67255604,5	MCF-7	breast:
5	chr12:67075881..67076642-chr12:67254630..67255196,2	MCF-7	breast:
6	chr12:67253715..67256707-chr12:67270307..67272731,2	K562	blood:
7	chr12:67253647..67256314-chr12:67565336..67566847,2	K562	blood:
8	chr12:67092019..67092945-chr12:67254522..67255578,9	MCF-7	breast:
9	chr12:67110471..67111538-chr12:67254403..67256131,14	MCF-7	breast:

No data

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10437935	0.81[AMR][1000 genomes]
rs10437969	0.81[AMR][1000 genomes]
rs10437970	0.81[AMR][1000 genomes]
rs10506502	0.81[AMR][1000 genomes]
rs10506504	0.81[AMR][1000 genomes]
rs10506506	0.81[AMR][1000 genomes]
rs10506507	0.81[AMR][1000 genomes]
rs11176441	0.81[AMR][1000 genomes]
rs11176445	0.81[AMR][1000 genomes]
rs11176446	0.81[AMR][1000 genomes]
rs11176447	0.81[AMR][1000 genomes]
rs11176455	0.82[ASN][1000 genomes]
rs12296450	0.81[AMR][1000 genomes]
rs12298007	0.81[AMR][1000 genomes]
rs12301508	0.81[AMR][1000 genomes]
rs12306322	0.81[AMR][1000 genomes]
rs12306499	0.81[AMR][1000 genomes]
rs12306766	0.81[AMR][1000 genomes]
rs12306768	0.81[AMR][1000 genomes]
rs12308379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309707	0.81[AMR][1000 genomes]
rs12309869	0.81[AMR][1000 genomes]
rs12311631	0.81[AMR][1000 genomes]
rs12311739	0.81[AMR][1000 genomes]
rs12313831	0.81[AMR][1000 genomes]
rs12316709	0.81[AMR][1000 genomes]
rs12318172	0.81[AMR][1000 genomes]
rs12319096	0.81[AMR][1000 genomes]
rs12319870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12320157	0.81[AMR][1000 genomes]
rs12320288	0.81[AMR][1000 genomes]
rs12322020	0.81[AMR][1000 genomes]
rs12322170	0.81[AMR][1000 genomes]
rs12579652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13377745	0.81[AMR][1000 genomes]
rs1504308	0.81[AMR][1000 genomes]
rs17247049	0.81[AMR][1000 genomes]
rs17827355	0.81[AMR][1000 genomes]
rs1921006	0.81[AMR][1000 genomes]
rs57685342	0.81[AMR][1000 genomes]
rs60903343	0.81[AMR][1000 genomes]
rs7957813	0.81[AMR][1000 genomes]
rs7971153	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1040682	chr12:66750103-67328053	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1053250	chr12:67067995-67381411	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1050547	chr12:67122154-67314886	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv541521	chr12:67122154-67314886	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1042117	chr12:67171949-67257435	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1038689	chr12:67174430-67257435	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1044061	chr12:67178298-67257941	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1037144	chr12:67203280-67325187	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1044939	chr12:67207260-67377982	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1045087	chr12:67225841-67257941	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv541522	chr12:67225841-67257941	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67253400-67255400	Enhancers	Primary T cells from cord blood	blood
2	chr12:67253400-67257800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:67253600-67255000	Enhancers	Fetal Heart	heart
4	chr12:67253800-67255000	Enhancers	Colon Smooth Muscle	Colon
5	chr12:67253800-67256800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:67254000-67255400	Enhancers	Rectal Smooth Muscle	rectum
7	chr12:67254200-67256400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:67254400-67256200	Enhancers	Fetal Brain Male	brain
9	chr12:67254600-67255200	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr12:67254600-67255400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr12:67254600-67255600	Enhancers	Fetal Brain Female	brain
12	chr12:67254600-67256000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:67254600-67256600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:67254800-67255400	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr12:67254800-67255400	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr12:67254800-67255400	Enhancers	Fetal Kidney	kidney
17	chr12:67254800-67256200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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