Variant report

Variant	rs12824125
Chromosome Location	chr12:50558974-50558975
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50495922..50498048-chr12:50556660..50559424,2	MCF-7	breast:
2	chr12:50549438..50552015-chr12:50558255..50560974,3	K562	blood:
3	chr12:50558904..50561005-chr12:50614879..50616650,2	MCF-7	breast:
4	chr12:50525406..50528688-chr12:50558864..50561981,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf62-2	chr12:50558809-50559203	ENSG00000272368.1

Variant related genes	Relation type
ENSG00000167588	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000050405	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1044370	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10747570	0.85[EUR][1000 genomes]
rs11169294	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169300	0.90[AMR][1000 genomes]
rs11831413	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12426261	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12815871	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12830386	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1862043	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2178173	0.86[EUR][1000 genomes]
rs34573394	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35549836	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35998534	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4883481	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4883482	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56709084	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6580729	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66768395	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7136570	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7279	0.89[EUR][1000 genomes]
rs7294548	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7297421	0.86[EUR][1000 genomes]
rs7301649	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7301740	0.86[EUR][1000 genomes]
rs7302981	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7308356	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7532	0.89[EUR][1000 genomes]
rs7967705	0.84[EUR][1000 genomes]
rs7967844	0.85[EUR][1000 genomes]
rs7972842	0.86[EUR][1000 genomes]
rs836179	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs836180	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12824125	CERS5	cis	Nerve Tibial	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50524000-50559800	Weak transcription	Right Atrium	heart
2	chr12:50529800-50559800	Weak transcription	NHLF	lung
3	chr12:50530000-50559600	Weak transcription	A549	lung
4	chr12:50530000-50560200	Weak transcription	Esophagus	oesophagus
5	chr12:50532000-50560200	Weak transcription	Aorta	Aorta
6	chr12:50532000-50560200	Weak transcription	Gastric	stomach
7	chr12:50532400-50559800	Weak transcription	Spleen	Spleen
8	chr12:50533200-50559400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:50534400-50560200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:50535200-50560000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:50535200-50560200	Weak transcription	Right Ventricle	heart
12	chr12:50535400-50559400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr12:50535400-50560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:50536400-50560200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:50537200-50559200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:50537400-50559400	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:50537400-50560200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:50537600-50559400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr12:50537600-50559400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr12:50537800-50559200	Weak transcription	GM12878-XiMat	blood
21	chr12:50537800-50559400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:50537800-50559400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:50537800-50559400	Weak transcription	Fetal Lung	lung
24	chr12:50537800-50559800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:50537800-50559800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:50537800-50560200	Weak transcription	Left Ventricle	heart
27	chr12:50538200-50559400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:50538200-50559800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr12:50538200-50559800	Weak transcription	Fetal Thymus	thymus
30	chr12:50538400-50559400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:50538400-50559400	Weak transcription	HSMM	muscle
32	chr12:50538400-50559400	Weak transcription	HSMMtube	muscle
33	chr12:50538400-50559800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr12:50540200-50559400	Weak transcription	Fetal Heart	heart
35	chr12:50542200-50559800	Weak transcription	Lung	lung
36	chr12:50543400-50559400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr12:50543400-50559600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr12:50545200-50560000	Weak transcription	Fetal Kidney	kidney
39	chr12:50546000-50559400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:50548000-50559200	Weak transcription	Thymus	Thymus
41	chr12:50548000-50559400	Weak transcription	NHEK	skin
42	chr12:50548000-50559800	Weak transcription	Fetal Muscle Leg	muscle
43	chr12:50548400-50559400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:50550200-50560200	Weak transcription	Small Intestine	intestine
45	chr12:50550800-50559400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:50551200-50560000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr12:50551600-50559200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr12:50551600-50559400	Weak transcription	NHDF-Ad	bronchial
49	chr12:50551600-50559800	Weak transcription	Primary B cells from cord blood	blood
50	chr12:50551600-50560000	Weak transcription	Liver	Liver

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