Variant report

Variant	rs613066
Chromosome Location	chr12:50454091-50454092
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50392906..50394750-chr12:50452166..50454470,2	MCF-7	breast:
2	chr12:50452539..50455408-chr12:50466138..50467868,2	MCF-7	breast:
3	chr12:50452088..50458692-chr12:50460164..50465883,8	K562	blood:
4	chr12:50360045..50361666-chr12:50451717..50454140,2	MCF-7	breast:
5	chr12:50453939..50455878-chr12:50478011..50480202,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161800	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000086159	Chromatin interaction

Extended variants
information (count: 34 )
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];1.00[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]
rs484951	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]
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]
rs627869	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627887	0.95[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];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs835594	0.86[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:8 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs613066	MICAL2	trans	lymphoblastoid	seeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50451400-50454400	Enhancers	Fetal Brain Male	brain
2	chr12:50451400-50459800	Weak transcription	Fetal Heart	heart
3	chr12:50451400-50464000	Weak transcription	Fetal Lung	lung
4	chr12:50451800-50454200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:50451800-50454200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:50451800-50464200	Weak transcription	Gastric	stomach
7	chr12:50452000-50454600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr12:50452000-50455000	Weak transcription	Right Atrium	heart
9	chr12:50452000-50456200	Weak transcription	HMEC	breast
10	chr12:50452000-50464200	Weak transcription	A549	lung
11	chr12:50452200-50454600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr12:50452200-50454600	Weak transcription	Adipose Nuclei	Adipose
13	chr12:50452200-50456400	Weak transcription	HSMM	muscle
14	chr12:50452200-50464000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:50452400-50454200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr12:50452400-50454400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr12:50452400-50455200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr12:50452400-50460200	Weak transcription	Hela-S3	cervix
19	chr12:50452600-50454200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:50452600-50454600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:50452600-50454800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:50452600-50456000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:50452600-50458200	Enhancers	Thymus	Thymus
24	chr12:50452600-50459200	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:50452600-50464000	Weak transcription	Esophagus	oesophagus
26	chr12:50452800-50454400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:50452800-50457200	Genic enhancers	Fetal Brain Female	brain
28	chr12:50452800-50458600	Enhancers	Fetal Thymus	thymus
29	chr12:50453000-50454200	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:50453000-50454400	Genic enhancers	Brain Inferior Temporal Lobe	brain
31	chr12:50453000-50454600	Strong transcription	Fetal Intestine Small	intestine
32	chr12:50453200-50454200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:50453200-50454400	Enhancers	Primary hematopoietic stem cells	blood
34	chr12:50453200-50454400	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr12:50453200-50454600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr12:50453200-50455200	Strong transcription	Stomach Smooth Muscle	stomach
37	chr12:50453200-50458400	Enhancers	Brain Substantia Nigra	brain
38	chr12:50453400-50454200	Flanking Active TSS	Dnd41	blood
39	chr12:50453400-50454200	Enhancers	NH-A	brain
40	chr12:50453400-50455200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:50453400-50455600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:50453400-50455600	Genic enhancers	Brain Hippocampus Middle	brain
43	chr12:50453600-50454200	Strong transcription	HSMMtube	muscle
44	chr12:50453600-50455000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr12:50453600-50455600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:50453600-50456400	Bivalent Enhancer	Placenta	Placenta
47	chr12:50453800-50455000	Enhancers	Primary T cells from cord blood	blood
48	chr12:50453800-50455200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr12:50453800-50455600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:50453800-50455800	Genic enhancers	Brain Angular Gyrus	brain

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