Variant report

Variant	rs7311958
Chromosome Location	chr12:57613425-57613426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr12:57612738-57615807	NT2-D1	testis:	n/a	n/a
2	CTBP2	chr12:57613144-57613612	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57608303..57611284-chr12:57611816..57613934,2	MCF-7	breast:

Variant related genes	Relation type
NXPH4	TF binding region
ENSG00000182379	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10783815	0.96[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs1140648	0.81[MKK][hapmap]
rs1800162	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1800164	0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1800168	0.81[MKK][hapmap]
rs7301155	0.88[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs7489231	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7956686	0.88[EUR][1000 genomes]
rs7956957	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7978567	0.84[CEU][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv559023	chr12:57530670-57616061	Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv525873	chr12:57535266-57616013	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	esv1809338	chr12:57580227-57628338	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv869636	chr12:57590172-57613714	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv899116	chr12:57597169-57623363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7311958	NPFF	cis	parietal	SCAN
rs7311958	NFE2	cis	cerebellum	SCAN
rs7311958	KRT71	cis	parietal	SCAN
rs7311958	OR6C1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57609800-57614600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:57611200-57613800	Bivalent Enhancer	Fetal Heart	heart
3	chr12:57611400-57613600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:57611400-57614600	Bivalent Enhancer	Fetal Lung	lung
5	chr12:57611400-57614600	Bivalent Enhancer	Fetal Stomach	stomach
6	chr12:57611400-57615400	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr12:57611400-57623000	Weak transcription	Right Atrium	heart
8	chr12:57611600-57613800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:57611800-57613600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:57611800-57614200	Weak transcription	Right Ventricle	heart
11	chr12:57611800-57615600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr12:57611800-57618400	Weak transcription	Pancreas	Pancrea
13	chr12:57612000-57614400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:57612600-57613600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
15	chr12:57612600-57614000	Bivalent Enhancer	Fetal Kidney	kidney
16	chr12:57612600-57617400	Bivalent Enhancer	Fetal Brain Male	brain
17	chr12:57612800-57613600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:57612800-57613600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:57612800-57613800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
20	chr12:57612800-57614600	Weak transcription	A549	lung
21	chr12:57612800-57616800	Bivalent Enhancer	Fetal Intestine Large	intestine
22	chr12:57612800-57618000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:57613000-57613800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:57613000-57614000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
25	chr12:57613200-57613600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
26	chr12:57613200-57613800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:57613200-57615800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
28	chr12:57613200-57621800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:57613400-57613600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:57613400-57613600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:57613400-57613600	Bivalent Enhancer	Brain Germinal Matrix	brain
32	chr12:57613400-57613800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
33	chr12:57613400-57613800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
34	chr12:57613400-57613800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:57613400-57614000	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:57613400-57615600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:57613400-57615800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:57613400-57620400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
39	chr12:57613400-57621600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

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