Variant report

Variant	rs4271437
Chromosome Location	chr12:9472643-9472644
allele	A/G
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	SPI1	chr12:9472029-9472724	GM12878	blood:	n/a	chr12:9472226-9472239 chr12:9472128-9472141 chr12:9472100-9472107
2	FOXA1	chr12:9472369-9472652	HepG2	liver:	n/a	n/a
3	PAX5	chr12:9471961-9472856	GM12878	blood:	n/a	n/a
4	TCF7L2	chr12:9472391-9472708	MCF-7	breast:	n/a	n/a
5	BHLHE40	chr12:9472155-9472656	GM12878	blood:	n/a	n/a
6	PAX5	chr12:9472094-9472663	GM12878	blood:	n/a	n/a
7	PAX5	chr12:9472150-9472645	GM12878	blood:	n/a	n/a
8	MTA3	chr12:9472049-9472722	GM12878	blood:	n/a	n/a
9	RUNX3	chr12:9472170-9472781	GM12878	blood:	n/a	n/a
10	SPI1	chr12:9472386-9472693	GM12891	blood:	n/a	n/a
11	POU2F2	chr12:9472063-9472731	GM12878	blood:	n/a	chr12:9472366-9472373
12	RUNX3	chr12:9472142-9472800	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9216104..9218306-chr12:9470179..9473467,3	MCF-7	breast:
2	chr12:9215714..9219195-chr12:9470456..9473261,3	MCF-7	breast:
3	chr12:9471764..9473665-chr12:9564371..9566160,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255753	TF binding region
ENSG00000214851	Chromatin interaction
ENSG00000245105	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1059171	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1059172	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10743654	0.80[CHD][hapmap];0.87[JPT][hapmap]
rs10743660	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743661	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771516	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs10771524	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10771531	0.93[ASN][1000 genomes]
rs10771532	0.81[ASN][1000 genomes]
rs10843360	0.81[JPT][hapmap]
rs10843400	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10843404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10843408	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843418	0.88[ASN][1000 genomes]
rs12303026	0.83[ASN][1000 genomes]
rs4589351	0.94[ASN][1000 genomes]
rs4883237	0.88[ASN][1000 genomes]
rs4883238	0.83[ASN][1000 genomes]
rs6487824	0.88[ASN][1000 genomes]
rs7299515	0.84[ASN][1000 genomes]
rs7311758	0.85[ASN][1000 genomes]
rs7954383	0.93[ASN][1000 genomes]
rs7957287	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	nsv916832	chr12:9397450-9693952	ZNF genes & repeats Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv976736	chr12:9431362-9524845	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv898740	chr12:9436446-9546962	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1050161	chr12:9436635-9685768	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv898741	chr12:9458525-9546962	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv976566	chr12:9469779-9481646	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1035958	chr12:9472365-9579109	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4271437	RP13-735L24.1	cis	Muscle Skeletal	GTEx
rs4271437	DDX12P	cis	Artery Tibial	GTEx
rs4271437	C12orf57	cis	cerebellum	SCAN
rs4271437	DDX12	cis	multi-tissue	Pritchard
rs4271437	RP11-22B23.1	cis	Muscle Skeletal	GTEx
rs4271437	RP11-22B23.1	cis	Artery Aorta	GTEx
rs4271437	RP11-22B23.1	cis	Whole Blood	GTEx
rs4271437	RP11-22B23.1	cis	Heart Left Ventricle	GTEx
rs4271437	RP11-22B23.1	cis	Thyroid	GTEx
rs4271437	RP11-22B23.1	cis	Artery Tibial	GTEx
rs4271437	RP11-22B23.1	cis	Esophagus Muscularis	GTEx
rs4271437	DDX12P	cis	Muscle Skeletal	GTEx
rs4271437	RP11-22B23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4271437	RP11-22B23.1	cis	lung	GTEx
rs4271437	SCNN1A	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9437200-9485200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:9457400-9485800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:9463000-9479000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:9464400-9477600	Weak transcription	Lung	lung
5	chr12:9464600-9487600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:9464800-9490000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:9465000-9473000	Weak transcription	Esophagus	oesophagus
8	chr12:9465000-9486400	Weak transcription	A549	lung
9	chr12:9465400-9485200	Weak transcription	Fetal Intestine Small	intestine
10	chr12:9465600-9477800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:9465600-9484000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:9465600-9488000	Weak transcription	Dnd41	blood
13	chr12:9466000-9484000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:9466200-9484000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:9466400-9477400	Weak transcription	Fetal Lung	lung
16	chr12:9466400-9485200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:9466400-9487200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:9466400-9487600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:9470000-9472800	Enhancers	HepG2	liver
20	chr12:9471600-9473000	Enhancers	Fetal Thymus	thymus
21	chr12:9471600-9473400	Enhancers	Primary B cells from peripheral blood	blood
22	chr12:9471800-9472800	Enhancers	Thymus	Thymus
23	chr12:9471800-9473000	Enhancers	Primary B cells from cord blood	blood
24	chr12:9471800-9473000	Enhancers	GM12878-XiMat	blood
25	chr12:9472000-9473000	Enhancers	Fetal Kidney	kidney
26	chr12:9472000-9473200	Enhancers	Stomach Mucosa	stomach
27	chr12:9472000-9473200	Enhancers	NHEK	skin
28	chr12:9472200-9472800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr12:9472200-9472800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:9472200-9473000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:9472200-9473200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:9472200-9476000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:9472400-9472800	Enhancers	HMEC	breast
34	chr12:9472400-9479400	Weak transcription	Brain Germinal Matrix	brain
35	chr12:9472600-9472800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr12:9472600-9472800	Enhancers	Primary T cells from cord blood	blood
37	chr12:9472600-9474000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr12:9472600-9475800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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