Variant report

Variant	rs2291920
Chromosome Location	chr12:278376-278377
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	CTCF	chr12:278320-278470	HAc	cerebellar:	n/a	n/a
2	RAD21	chr12:278336-279099	H1-hESC	embryonic stem cell:	n/a	chr12:279077-279090 chr12:278740-278750 chr12:278560-278573 chr12:278799-278806
3	E2F6	chr12:278335-278866	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000256694	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10505717	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744538	0.94[ASN][1000 genomes]
rs10773937	0.92[ASN][1000 genomes]
rs10848481	0.88[ASN][1000 genomes]
rs11061708	0.89[ASN][1000 genomes]
rs11061709	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368193	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17692962	0.99[ASN][1000 genomes]
rs183355	0.88[ASN][1000 genomes]
rs216227	0.88[ASN][1000 genomes]
rs2291917	0.87[ASN][1000 genomes]
rs2291918	0.92[ASN][1000 genomes]
rs2291919	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291921	0.97[EUR][1000 genomes]
rs2291922	0.96[EUR][1000 genomes]
rs2291923	0.96[EUR][1000 genomes]
rs3817016	0.84[EUR][1000 genomes]
rs3847946	0.83[EUR][1000 genomes]
rs3892665	0.88[ASN][1000 genomes]
rs3902268	0.81[EUR][1000 genomes]
rs3902269	0.83[EUR][1000 genomes]
rs4980859	0.96[EUR][1000 genomes]
rs502783	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs505387	0.89[ASN][1000 genomes]
rs559759	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs565091	0.83[ASN][1000 genomes]
rs57052808	0.89[ASN][1000 genomes]
rs61907087	0.86[ASN][1000 genomes]
rs61907088	0.85[ASN][1000 genomes]
rs633159	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7959974	0.84[CHB][hapmap];0.87[CHD][hapmap]
rs7960096	0.84[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs7967899	0.87[ASN][1000 genomes]
rs7967909	0.85[ASN][1000 genomes]
rs7971499	0.87[ASN][1000 genomes]
rs797736	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv983433	chr12:145740-400932	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv427901	chr12:146333-344299	Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv428269	chr12:146333-344299	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1041243	chr12:150430-310571	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1038621	chr12:150430-324923	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv898552	chr12:154752-303320	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2291920	ITFG2	cis	parietal	SCAN
rs2291920	ZSCAN18	trans	parietal	SCAN
rs2291920	IQSEC3	cis	parietal	SCAN
rs2291920	PARP11	cis	cerebellum	SCAN
rs2291920	HM13	trans	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:249000-284200	Weak transcription	Right Atrium	heart
2	chr12:253800-285600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:262800-284200	Weak transcription	Brain Angular Gyrus	brain
4	chr12:266200-280000	Weak transcription	Right Ventricle	heart
5	chr12:268800-284200	Weak transcription	Brain Anterior Caudate	brain
6	chr12:273000-279400	Enhancers	Fetal Intestine Small	intestine
7	chr12:273000-281000	Weak transcription	Colonic Mucosa	Colon
8	chr12:273200-279000	Enhancers	Fetal Intestine Large	intestine
9	chr12:273600-284600	Weak transcription	Esophagus	oesophagus
10	chr12:273800-278400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:275000-279000	Enhancers	Fetal Thymus	thymus
12	chr12:275200-278400	Enhancers	Duodenum Mucosa	Duodenum
13	chr12:276200-282800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:276200-284000	Enhancers	Primary hematopoietic stem cells	blood
15	chr12:276400-278600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr12:276400-278600	Enhancers	Left Ventricle	heart
17	chr12:276400-280200	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr12:276400-281000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr12:276400-283000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:276600-279800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr12:277000-278400	Enhancers	Fetal Kidney	kidney
22	chr12:277200-279400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:277200-292800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:277400-280200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr12:277400-283200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:277600-278600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:277600-278800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:277600-280000	Enhancers	H9 Cell Line	embryonic stem cell
29	chr12:277600-280800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr12:277600-280800	Weak transcription	Stomach Mucosa	stomach
31	chr12:277600-281000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr12:277800-278400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr12:277800-278400	Weak transcription	Fetal Heart	heart
34	chr12:277800-278400	Enhancers	GM12878-XiMat	blood
35	chr12:277800-278600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:277800-278600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
37	chr12:277800-278600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:277800-278800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:277800-278800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr12:277800-278800	Enhancers	HSMMtube	muscle
41	chr12:277800-279200	Enhancers	HSMM	muscle
42	chr12:277800-279800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:277800-279800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr12:277800-280000	Enhancers	NH-A	brain
45	chr12:277800-280800	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr12:277800-282400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:278000-278400	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr12:278000-278400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr12:278000-278400	Enhancers	Liver	Liver
50	chr12:278000-278600	Enhancers	Primary T helper cells fromperipheralblood	blood

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