Variant report

Variant	rs12930612
Chromosome Location	chr16:12072203-12072204
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr16:12069635-12072270	IMR90	lung:	n/a	chr16:12070760-12070770
2	MTA3	chr16:12071683-12072512	GM12878	blood:	n/a	n/a
3	CTCF	chr16:12072140-12072290	MCF-7	breast:	n/a	n/a
4	CTCF	chr16:12072080-12072230	GM12872	blood:	n/a	n/a
5	CTCF	chr16:12072140-12072290	AG09319	gingival:	n/a	n/a
6	MTA3	chr16:12072043-12072490	GM12878	blood:	n/a	n/a
7	WRNIP1	chr16:12070864-12072578	GM12878	blood:	n/a	n/a
8	TBP	chr16:12072106-12072631	GM12878	blood:	n/a	chr16:12072456-12072467
9	POLR2A	chr16:12072044-12072470	GM12891	blood:	n/a	n/a
10	POLR2A	chr16:12072085-12072384	GM12878	blood:	n/a	n/a
11	POLR2A	chr16:12069293-12072542	GM12891	blood:	n/a	n/a
12	POLR2A	chr16:12071954-12072527	GM12878	blood:	n/a	n/a
13	ELK1	chr16:12071980-12072225	GM12878	blood:	n/a	n/a
14	CTCF	chr16:12072080-12072230	RPTEC	kidney:	n/a	n/a
15	TBL1XR1	chr16:12071822-12072529	GM12878	blood:	n/a	n/a
16	MXI1	chr16:12072178-12072658	GM12878	blood:	n/a	n/a
17	CTCF	chr16:12072080-12072230	HBMEC	blood vessel:	n/a	n/a
18	CTCF	chr16:12072060-12072210	HVMF	connective:	n/a	n/a
19	MXI1	chr16:12069562-12072323	SK-N-SH	brain:	n/a	n/a
20	CTCF	chr16:12072060-12072210	GM12865	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:12006809..12011472-chr16:12069677..12072698,7	MCF-7	breast:
2	chr16:12071974..12074044-chr16:12076209..12078195,2	K562	blood:
3	chr16:12070324..12072776-chr16:12897424..12899893,2	K562	blood:
4	chr16:12058363..12061770-chr16:12069205..12072370,4	MCF-7	breast:
5	chr16:12069629..12072468-chr16:12173207..12175470,2	MCF-7	breast:
6	chr16:12068621..12072204-chr16:12129850..12134239,5	MCF-7	breast:
7	chr16:12006532..12011371-chr16:12068460..12073371,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000234719	TF binding region
ENSG00000260488	TF binding region
ENSG00000048462	Chromatin interaction
ENSG00000266163	Chromatin interaction
ENSG00000103342	Chromatin interaction
ENSG00000103381	Chromatin interaction
ENSG00000048471	Chromatin interaction
ENSG00000241641	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11859104	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12922317	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16958789	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16958792	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28473763	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2869492	0.84[AMR][1000 genomes]
rs34959638	0.91[EUR][1000 genomes]
rs3851005	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs393329	0.82[AMR][1000 genomes]
rs67163308	0.87[EUR][1000 genomes]
rs7206479	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8043644	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8061496	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv527197	chr16:12071341-12073800	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12930612	RP11-166B2.1	cis	Nerve Tibial	GTEx
rs12930612	RP11-166B2.1	cis	Adipose Subcutaneous	GTEx
rs12930612	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12930612	RP11-166B2.1	cis	Thyroid	GTEx
rs12930612	RP11-166B2.1	cis	Artery Tibial	GTEx
rs12930612	RP11-166B2.1	cis	Esophagus Muscularis	GTEx
rs12930612	RP11-166B2.1	cis	Heart Left Ventricle	GTEx
rs12930612	RP11-166B2.1	cis	Stomach	GTEx
rs12930612	RP11-166B2.1	cis	Whole Blood	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12069600-12072600	Active TSS	Fetal Kidney	kidney
2	chr16:12070000-12072400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr16:12070200-12072400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr16:12070800-12072400	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr16:12070800-12072600	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr16:12071000-12072600	Flanking Active TSS	Primary B cells from peripheral blood	blood
7	chr16:12071400-12072400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr16:12071400-12130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr16:12071600-12072400	Enhancers	Placenta	Placenta
10	chr16:12071600-12072600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr16:12071600-12072600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr16:12071600-12072600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr16:12071600-12072600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr16:12071600-12072600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr16:12071600-12072800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr16:12071600-12083200	Weak transcription	Left Ventricle	heart
17	chr16:12071800-12072400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr16:12071800-12072400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr16:12071800-12072400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr16:12071800-12072400	Enhancers	Brain Angular Gyrus	brain
21	chr16:12071800-12072600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr16:12071800-12072600	Enhancers	Brain Anterior Caudate	brain
23	chr16:12071800-12072600	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr16:12071800-12072600	Enhancers	Rectal Smooth Muscle	rectum
25	chr16:12071800-12072600	Flanking Active TSS	NHDF-Ad	bronchial
26	chr16:12071800-12078000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr16:12071800-12079400	Weak transcription	Lung	lung
28	chr16:12071800-12079800	Weak transcription	Aorta	Aorta
29	chr16:12071800-12083200	Weak transcription	Spleen	Spleen
30	chr16:12071800-12088200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
32	chr16:12072000-12072400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr16:12072000-12072400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr16:12072000-12072400	Enhancers	Primary T cells from cord blood	blood
35	chr16:12072000-12072400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr16:12072000-12072400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr16:12072000-12072400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr16:12072000-12072400	Enhancers	Adipose Nuclei	Adipose
39	chr16:12072000-12072400	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr16:12072000-12072400	Enhancers	Ovary	ovary
41	chr16:12072000-12072400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr16:12072000-12072400	Enhancers	Dnd41	blood
43	chr16:12072000-12072400	Enhancers	Hela-S3	cervix
44	chr16:12072000-12072400	Enhancers	K562	blood
45	chr16:12072000-12072400	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr16:12072000-12072400	Enhancers	NHEK	skin
47	chr16:12072000-12072600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr16:12072000-12072600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr16:12072000-12072600	Enhancers	Brain Cingulate Gyrus	brain
50	chr16:12072000-12072600	Enhancers	Brain Inferior Temporal Lobe	brain

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