Variant report

Variant	rs2291921
Chromosome Location	chr12:275270-275271
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC6A12-2	chr12:274478-275487	ENSG00000256694.1

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10505717	0.97[EUR][1000 genomes]
rs11061709	0.97[EUR][1000 genomes]
rs12368193	0.98[EUR][1000 genomes]
rs2291919	0.81[EUR][1000 genomes]
rs2291920	0.97[EUR][1000 genomes]
rs2291922	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291923	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817016	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3847946	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3902268	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3902269	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4980859	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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

No data

Chromatin state (count:29 , 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	chr12:262800-277000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:262800-284200	Weak transcription	Brain Angular Gyrus	brain
5	chr12:266200-280000	Weak transcription	Right Ventricle	heart
6	chr12:268800-284200	Weak transcription	Brain Anterior Caudate	brain
7	chr12:271600-277600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:272400-275400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:272400-278200	Weak transcription	Fetal Brain Female	brain
10	chr12:273000-276400	Weak transcription	Left Ventricle	heart
11	chr12:273000-279400	Enhancers	Fetal Intestine Small	intestine
12	chr12:273000-281000	Weak transcription	Colonic Mucosa	Colon
13	chr12:273200-275400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:273200-279000	Enhancers	Fetal Intestine Large	intestine
15	chr12:273600-277400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:273600-277600	Weak transcription	Brain Germinal Matrix	brain
17	chr12:273600-284600	Weak transcription	Esophagus	oesophagus
18	chr12:273800-276800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:273800-278200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:273800-278400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:274000-277000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:274000-277200	Weak transcription	Stomach Mucosa	stomach
23	chr12:274400-275400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:274400-276400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:274400-277000	Weak transcription	Fetal Kidney	kidney
26	chr12:274600-275600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:275000-279000	Enhancers	Fetal Thymus	thymus
28	chr12:275200-276000	Enhancers	GM12878-XiMat	blood
29	chr12:275200-278400	Enhancers	Duodenum Mucosa	Duodenum

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