Variant report

Variant	rs12452961
Chromosome Location	chr17:33908649-33908650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:33903370..33909494-chr17:33910892..33920548,27	MCF-7	breast:
2	chr17:33903997..33907288-chr17:33908412..33910770,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006125	Chromatin interaction
ENSG00000108733	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1037591	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10491114	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10491115	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11870399	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870475	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12449919	0.92[ASN][1000 genomes]
rs12450039	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12452633	0.81[ASN][1000 genomes]
rs12600662	0.81[ASN][1000 genomes]
rs12603142	0.97[ASN][1000 genomes]
rs1964509	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs226433	0.92[ASN][1000 genomes]
rs226435	0.92[ASN][1000 genomes]
rs226436	0.92[ASN][1000 genomes]
rs226437	0.92[ASN][1000 genomes]
rs2278950	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2301731	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2428463	0.92[ASN][1000 genomes]
rs2523115	0.92[ASN][1000 genomes]
rs28384428	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28384429	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661650	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3760325	0.92[ASN][1000 genomes]
rs3785759	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3785763	0.97[ASN][1000 genomes]
rs62079728	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7211363	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9303689	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9891317	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9904957	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9906037	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914730	0.97[ASN][1000 genomes]
rs9916483	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	esv3392862	chr17:33907589-33909537	Weak transcription	TF binding region CpG island Chromatin interactive region	4 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	chr17:33906400-33913800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:33906400-33913800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:33906600-33910600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr17:33906600-33911000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:33906600-33913400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr17:33906600-33913400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr17:33906600-33913400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr17:33906600-33913400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:33906600-33913400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr17:33906600-33913400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr17:33906600-33913400	Weak transcription	Liver	Liver
12	chr17:33906600-33913400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr17:33906600-33913400	Weak transcription	NHEK	skin
14	chr17:33906600-33913800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr17:33906600-33914000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr17:33906800-33910600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr17:33906800-33911000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr17:33906800-33913600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr17:33907200-33913600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr17:33907200-33913800	Weak transcription	HepG2	liver
21	chr17:33907400-33911400	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links