Variant report

Variant	rs484951
Chromosome Location	chr12:50458073-50458074
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50449783..50453110-chr12:50454636..50460246,5	MCF-7	breast:
2	chr12:50431118..50433234-chr12:50455949..50458611,2	MCF-7	breast:
3	chr12:50452088..50458692-chr12:50460164..50465883,8	K562	blood:

Variant related genes	Relation type
ENSG00000110881	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs17124514	1.00[CEU][hapmap]
rs2307084	0.82[JPT][hapmap]
rs376184	0.80[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs386469	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs393848	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs404751	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs439171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs450423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4898546	0.80[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs590460	0.80[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs613066	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627869	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627887	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs653576	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs685012	0.90[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap]
rs706789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs706794	0.80[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs835591	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs835593	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs835594	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs836178	0.92[JPT][hapmap]
rs836184	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs836185	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs836186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844359	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs860699	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	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
4	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	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
8	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv437753	chr12:50454357-50462138	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs484951	MICAL2	trans	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50451400-50459800	Weak transcription	Fetal Heart	heart
2	chr12:50451400-50464000	Weak transcription	Fetal Lung	lung
3	chr12:50451800-50464200	Weak transcription	Gastric	stomach
4	chr12:50452000-50464200	Weak transcription	A549	lung
5	chr12:50452200-50464000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:50452400-50460200	Weak transcription	Hela-S3	cervix
7	chr12:50452600-50458200	Enhancers	Thymus	Thymus
8	chr12:50452600-50459200	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:50452600-50464000	Weak transcription	Esophagus	oesophagus
10	chr12:50452800-50458600	Enhancers	Fetal Thymus	thymus
11	chr12:50453200-50458400	Enhancers	Brain Substantia Nigra	brain
12	chr12:50453800-50460400	Strong transcription	Fetal Stomach	stomach
13	chr12:50454400-50459600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:50454400-50460000	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr12:50454600-50464200	Weak transcription	Fetal Intestine Small	intestine
16	chr12:50454800-50458800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:50454800-50464000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:50455000-50459800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:50455400-50459600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:50455400-50459600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:50455600-50458800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr12:50455600-50459600	Enhancers	Brain Hippocampus Middle	brain
23	chr12:50455600-50464200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:50455800-50458600	Enhancers	Brain Angular Gyrus	brain
25	chr12:50455800-50464000	Weak transcription	Adipose Nuclei	Adipose
26	chr12:50456000-50459600	Weak transcription	Right Atrium	heart
27	chr12:50456000-50460800	Enhancers	Fetal Muscle Leg	muscle
28	chr12:50456200-50459200	Weak transcription	Primary T cells from cord blood	blood
29	chr12:50456600-50463800	Weak transcription	Dnd41	blood
30	chr12:50456800-50459600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:50456800-50460000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr12:50457200-50459400	Strong transcription	Fetal Brain Female	brain
33	chr12:50457200-50459600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:50457200-50459600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:50457200-50460000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:50457200-50460000	Weak transcription	NH-A	brain
37	chr12:50457400-50460000	Weak transcription	HSMM	muscle
38	chr12:50457400-50464000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:50457600-50458400	Genic enhancers	Brain Anterior Caudate	brain
40	chr12:50457600-50458600	Strong transcription	Brain Germinal Matrix	brain
41	chr12:50457600-50459000	Weak transcription	Fetal Brain Male	brain
42	chr12:50457600-50459600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:50457800-50458200	Weak transcription	HSMMtube	muscle
44	chr12:50458000-50458200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:50458000-50458400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:50458000-50458600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr12:50458000-50461600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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