Variant report

Variant	rs17692962
Chromosome Location	chr12:277464-277465
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10505717	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1051104	0.80[CHD][hapmap]
rs10744538	0.95[ASN][1000 genomes]
rs10773937	0.92[ASN][1000 genomes]
rs10848481	0.87[ASN][1000 genomes]
rs11061708	0.90[ASN][1000 genomes]
rs11061709	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12368193	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs183355	0.87[ASN][1000 genomes]
rs2075228	0.80[CHD][hapmap]
rs216227	0.87[ASN][1000 genomes]
rs2291917	0.88[ASN][1000 genomes]
rs2291918	0.93[ASN][1000 genomes]
rs2291919	0.92[ASN][1000 genomes]
rs2291920	0.99[ASN][1000 genomes]
rs3892665	0.87[ASN][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]
rs515932	0.80[CHD][hapmap]
rs542736	0.80[CHD][hapmap]
rs559759	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs565091	0.83[ASN][1000 genomes]
rs57052808	0.88[ASN][1000 genomes]
rs61907087	0.85[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];0.88[CHD][hapmap]
rs7960096	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs7967899	0.86[ASN][1000 genomes]
rs7967909	0.85[ASN][1000 genomes]
rs7971499	0.87[ASN][1000 genomes]
rs797736	0.88[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
rs17692962	IQSEC3	cis	parietal	SCAN
rs17692962	ITFG2	cis	parietal	SCAN
rs17692962	HM13	trans	parietal	SCAN
rs17692962	PARP11	cis	cerebellum	SCAN
rs17692962	ZSCAN18	trans	parietal	SCAN

Chromatin state (count:40 , 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	chr12:266200-280000	Weak transcription	Right Ventricle	heart
5	chr12:268800-284200	Weak transcription	Brain Anterior Caudate	brain
6	chr12:271600-277600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:272400-278200	Weak transcription	Fetal Brain Female	brain
8	chr12:273000-279400	Enhancers	Fetal Intestine Small	intestine
9	chr12:273000-281000	Weak transcription	Colonic Mucosa	Colon
10	chr12:273200-279000	Enhancers	Fetal Intestine Large	intestine
11	chr12:273600-277600	Weak transcription	Brain Germinal Matrix	brain
12	chr12:273600-284600	Weak transcription	Esophagus	oesophagus
13	chr12:273800-278200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:273800-278400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:275000-279000	Enhancers	Fetal Thymus	thymus
16	chr12:275200-278400	Enhancers	Duodenum Mucosa	Duodenum
17	chr12:275400-278000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:276000-277800	Weak transcription	GM12878-XiMat	blood
19	chr12:276200-282800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:276200-284000	Enhancers	Primary hematopoietic stem cells	blood
21	chr12:276400-278600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr12:276400-278600	Enhancers	Left Ventricle	heart
23	chr12:276400-280200	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr12:276400-281000	Enhancers	H1 Cell Line	embryonic stem cell
25	chr12:276400-283000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:276600-279800	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr12:276800-277800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:276800-278000	Weak transcription	Liver	Liver
29	chr12:277000-277600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:277000-277600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:277000-277800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:277000-278000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:277000-278400	Enhancers	Fetal Kidney	kidney
34	chr12:277200-277600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:277200-277600	Enhancers	Stomach Mucosa	stomach
36	chr12:277200-279400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:277200-292800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:277400-277600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:277400-280200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr12:277400-283200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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