Variant report

Variant	rs2291919
Chromosome Location	chr12:280349-280350
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:278455..281013-chr12:283457..285093,2	K562	blood:
2	chr12:276004..278175-chr12:278500..282427,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120645	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10505717	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1051104	0.80[CHD][hapmap]
rs10744538	0.87[ASN][1000 genomes]
rs10773937	0.85[ASN][1000 genomes]
rs10848481	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11061708	0.82[ASN][1000 genomes]
rs11061709	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12366364	0.87[AFR][1000 genomes]
rs12368193	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17692962	0.92[ASN][1000 genomes]
rs183355	0.83[ASN][1000 genomes]
rs2075228	0.80[CHD][hapmap]
rs216227	0.83[ASN][1000 genomes]
rs2291917	0.94[ASN][1000 genomes]
rs2291918	0.86[ASN][1000 genomes]
rs2291920	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291921	0.81[EUR][1000 genomes]
rs2291922	0.81[EUR][1000 genomes]
rs2291923	0.81[EUR][1000 genomes]
rs3892665	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4980859	0.81[EUR][1000 genomes]
rs502783	0.90[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs505387	0.84[ASN][1000 genomes]
rs515932	0.80[CHD][hapmap]
rs542736	0.80[CHD][hapmap]
rs57052808	0.84[ASN][1000 genomes]
rs61907087	0.81[ASN][1000 genomes]
rs61907088	0.80[ASN][1000 genomes]
rs633159	0.90[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs7959974	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs7960096	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7967899	0.82[ASN][1000 genomes]
rs7967909	0.80[ASN][1000 genomes]
rs7971499	0.82[ASN][1000 genomes]
rs797736	0.84[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
rs2291919	ZSCAN18	trans	parietal	SCAN
rs2291919	ITFG2	cis	parietal	SCAN
rs2291919	PARP11	cis	cerebellum	SCAN
rs2291919	IQSEC3	cis	parietal	SCAN
rs2291919	HM13	trans	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

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	chr12:268800-284200	Weak transcription	Brain Anterior Caudate	brain
5	chr12:273000-281000	Weak transcription	Colonic Mucosa	Colon
6	chr12:273600-284600	Weak transcription	Esophagus	oesophagus
7	chr12:276200-282800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:276200-284000	Enhancers	Primary hematopoietic stem cells	blood
9	chr12:276400-281000	Enhancers	H1 Cell Line	embryonic stem cell
10	chr12:276400-283000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:277200-292800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:277400-283200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:277600-280800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr12:277600-280800	Weak transcription	Stomach Mucosa	stomach
15	chr12:277600-281000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr12:277800-280800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr12:277800-282400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:278400-280600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr12:278400-283400	Weak transcription	Liver	Liver
20	chr12:278400-283600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:278400-288400	Weak transcription	Fetal Kidney	kidney
22	chr12:278600-280400	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr12:278600-280800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
24	chr12:278600-281000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:278600-281000	Weak transcription	Left Ventricle	heart
26	chr12:278600-282200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr12:278600-283400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:278800-280600	Weak transcription	Fetal Stomach	stomach
29	chr12:278800-280800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:279000-280600	Weak transcription	Fetal Heart	heart
31	chr12:279000-281200	Weak transcription	Fetal Intestine Large	intestine
32	chr12:279000-285200	Weak transcription	Fetal Thymus	thymus
33	chr12:279200-281000	Weak transcription	HSMM	muscle
34	chr12:279400-280600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:279400-280600	Weak transcription	Fetal Intestine Small	intestine
36	chr12:279400-281000	Weak transcription	HSMMtube	muscle
37	chr12:279800-283400	Weak transcription	Fetal Lung	lung
38	chr12:280000-280400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:280000-280400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:280000-282200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:280000-283000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:280000-286000	Weak transcription	Fetal Brain Female	brain
43	chr12:280000-289600	Enhancers	Right Ventricle	heart

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