Variant report

Variant	rs3956833
Chromosome Location	chr12:120705828-120705829
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:120705665-120705959	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr12:120705543-120705909	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr12:120705548-120706118	HUVEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:120699116..120708865-chr12:120725013..120732311,37	K562	blood:
2	chr12:120697928..120706288-chr12:120725352..120732223,30	K562	blood:
3	chr12:120553785..120557408-chr12:120702135..120705915,4	K562	blood:
4	chr12:120703812..120708110-chr12:120710658..120713817,5	MCF-7	breast:
5	chr12:120690051..120707499-chr12:120720410..120732530,91	MCF-7	breast:
6	chr12:120686978..120689816-chr12:120703862..120706218,2	K562	blood:
7	chr12:120704439..120706873-chr12:120717613..120720324,2	MCF-7	breast:
8	chr12:120636814..120640513-chr12:120703939..120707132,3	K562	blood:
9	chr12:120629843..120633670-chr12:120702168..120705891,5	K562	blood:

No data

Variant related genes	Relation type
PXN	TF binding region
ENSG00000111737	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000123009	Chromatin interaction
ENSG00000089159	Chromatin interaction
ENSG00000089154	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000255857	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10849739	0.91[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11065028	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs11065061	0.91[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11065064	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1151824	0.91[CEU][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs1151825	0.91[CEU][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs1151827	0.91[CEU][hapmap];0.98[EUR][1000 genomes]
rs1151830	0.94[EUR][1000 genomes]
rs1151832	0.91[CEU][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs1151837	0.88[CEU][hapmap];0.98[EUR][1000 genomes]
rs1182860	0.98[EUR][1000 genomes]
rs11831552	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1183781	0.88[CEU][hapmap];0.98[EUR][1000 genomes]
rs12164847	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12305146	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12308431	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12321884	0.80[AMR][1000 genomes]
rs12581983	0.81[AMR][1000 genomes]
rs1634814	0.91[CEU][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs1634815	0.91[CEU][hapmap];0.98[EUR][1000 genomes]
rs2006194	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2238156	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2238157	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2239208	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240315	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2269940	0.91[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs2283364	0.83[CEU][hapmap];0.80[AMR][1000 genomes]
rs2283365	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2286044	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2524391	0.98[EUR][1000 genomes]
rs3759397	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3888587	0.91[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3888588	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3890165	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4767886	0.91[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61198412	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7300273	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs739809	0.91[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7953949	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7966099	0.91[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[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	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
2	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases
3	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
4	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers 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	436 gene(s)	inside rSNPs	diseases
5	nsv560435	chr12:120695141-120769657	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	433 gene(s)	inside rSNPs	diseases
6	nsv899556	chr12:120695141-120779931	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	433 gene(s)	inside rSNPs	diseases
7	nsv560436	chr12:120697470-120705828	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3956833	FBXO21	cis	parietal	SCAN
rs3956833	HRK	cis	parietal	SCAN
rs3956833	PXN	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120704000-120706400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:120704000-120706800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:120704000-120721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:120704400-120714400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:120704600-120714200	Weak transcription	Placenta	Placenta
6	chr12:120705000-120706600	Enhancers	Fetal Intestine Large	intestine
7	chr12:120705000-120706800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr12:120705200-120706000	Enhancers	Fetal Lung	lung
9	chr12:120705200-120706200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr12:120705200-120706400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr12:120705200-120706400	Enhancers	Liver	Liver
12	chr12:120705200-120706400	Enhancers	Colonic Mucosa	Colon
13	chr12:120705200-120706400	Enhancers	HUVEC	blood vessel
14	chr12:120705200-120706800	Enhancers	Duodenum Mucosa	Duodenum
15	chr12:120705400-120706000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr12:120705400-120706000	Enhancers	Fetal Stomach	stomach
17	chr12:120705400-120706400	Enhancers	Fetal Intestine Small	intestine
18	chr12:120705400-120706800	Enhancers	Stomach Mucosa	stomach
19	chr12:120705600-120706000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr12:120705600-120706000	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:120705600-120706000	Enhancers	Adipose Nuclei	Adipose
22	chr12:120705600-120706000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr12:120705600-120706200	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr12:120705600-120706200	Enhancers	Primary hematopoietic stem cells	blood
25	chr12:120705600-120706200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:120705600-120706200	Flanking Active TSS	HepG2	liver
27	chr12:120705800-120707400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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