Variant report

Variant	rs56236944
Chromosome Location	chr12:9469846-9469847
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	POLR2A	chr12:9469822-9470214	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:9469157-9470039	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr12:9469763-9470122	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:9469573-9469942	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000255753	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10843459	1.00[ASN][1000 genomes]
rs11050246	1.00[ASN][1000 genomes]
rs11050254	0.89[ASN][1000 genomes]
rs11050303	1.00[ASN][1000 genomes]
rs11050304	1.00[ASN][1000 genomes]
rs11050310	1.00[ASN][1000 genomes]
rs11050397	0.89[ASN][1000 genomes]
rs11050527	0.89[ASN][1000 genomes]
rs11050586	0.89[ASN][1000 genomes]
rs11050592	0.89[ASN][1000 genomes]
rs11050604	0.89[ASN][1000 genomes]
rs11050605	0.89[ASN][1000 genomes]
rs12370449	0.89[ASN][1000 genomes]
rs12372791	0.89[ASN][1000 genomes]
rs17804845	0.89[ASN][1000 genomes]
rs17804911	0.89[ASN][1000 genomes]
rs2113904	0.89[ASN][1000 genomes]
rs2194829	0.89[ASN][1000 genomes]
rs34591612	0.89[ASN][1000 genomes]
rs36132622	0.89[ASN][1000 genomes]
rs4883242	1.00[ASN][1000 genomes]
rs55635549	0.89[ASN][1000 genomes]
rs55693818	0.89[ASN][1000 genomes]
rs56004061	0.89[ASN][1000 genomes]
rs56014159	1.00[ASN][1000 genomes]
rs7295431	1.00[ASN][1000 genomes]
rs7302181	1.00[ASN][1000 genomes]
rs73047561	1.00[ASN][1000 genomes]
rs7486338	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	esv3367784	chr12:9466785-9470133	Weak transcription Enhancers	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv8904	chr12:9468460-9470499	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56236944	DDX11///DDX12///LOC642846	Cis_chr	lymphoblastoid	RTeQTL
rs56236944	LOC728715///OVOS2	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9437200-9472400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr12:9437200-9485200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:9437400-9470800	Weak transcription	Brain Germinal Matrix	brain
4	chr12:9450200-9471400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr12:9456200-9472200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:9456400-9471800	Weak transcription	GM12878-XiMat	blood
7	chr12:9457400-9485800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:9458000-9472200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:9463000-9479000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:9463200-9471600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:9464400-9477600	Weak transcription	Lung	lung
12	chr12:9464600-9487600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:9464800-9472200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:9464800-9472200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:9464800-9490000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:9465000-9472600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:9465000-9473000	Weak transcription	Esophagus	oesophagus
18	chr12:9465000-9486400	Weak transcription	A549	lung
19	chr12:9465200-9471400	Weak transcription	Spleen	Spleen
20	chr12:9465400-9485200	Weak transcription	Fetal Intestine Small	intestine
21	chr12:9465600-9471000	Weak transcription	Fetal Stomach	stomach
22	chr12:9465600-9472200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:9465600-9477800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:9465600-9484000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:9465600-9488000	Weak transcription	Dnd41	blood
26	chr12:9466000-9484000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:9466200-9472400	Weak transcription	HMEC	breast
28	chr12:9466200-9484000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:9466400-9470200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:9466400-9471600	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:9466400-9471600	Weak transcription	Fetal Thymus	thymus
32	chr12:9466400-9471800	Weak transcription	Thymus	Thymus
33	chr12:9466400-9472000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:9466400-9477400	Weak transcription	Fetal Lung	lung
35	chr12:9466400-9485200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:9466400-9487200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:9466400-9487600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:9466600-9470000	Weak transcription	HepG2	liver
39	chr12:9468800-9471000	Weak transcription	Fetal Muscle Trunk	muscle

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