Variant report

Variant	rs28512322
Chromosome Location	chr16:12069839-12069840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	POLR2A	chr16:12069402-12071168	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:12069631-12070837	K562	blood:	n/a	n/a
4	POLR2A	chr16:12069350-12071988	GM12878	blood:	n/a	n/a
5	FOSL2	chr16:12069545-12070262	A549	lung:	n/a	n/a
6	SMARCB1	chr16:12069661-12071538	Hela-S3	cervix:	n/a	n/a
7	RFX5	chr16:12069574-12069978	Hela-S3	cervix:	n/a	n/a
8	CHD2	chr16:12069658-12069974	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr16:12069698-12071959	IMR90	lung:	n/a	n/a
10	NR2F2	chr16:12069539-12070406	K562	blood:	n/a	n/a
11	POLR2A	chr16:12069510-12071691	MCF10A-Er-Src	breast:	n/a	n/a
12	TBL1XR1	chr16:12069726-12069839	K562	blood:	n/a	n/a
13	HEY1	chr16:12069646-12070819	K562	blood:	n/a	chr16:12070718-12070733 chr16:12070709-12070724
14	RCOR1	chr16:12069610-12071817	K562	blood:	n/a	n/a
15	JUN	chr16:12069540-12069909	K562	blood:	n/a	n/a
16	GTF3C2	chr16:12069473-12070432	Hela-S3	cervix:	n/a	n/a
17	FOSL2	chr16:12069597-12070000	MCF-7	breast:	n/a	n/a
18	GTF2F1	chr16:12069641-12070501	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr16:12069616-12071570	GM19193	blood:	n/a	n/a
20	POLR2A	chr16:12069559-12071042	K562	blood:	n/a	n/a
21	GABPA	chr16:12069823-12070904	K562	blood:	n/a	chr16:12070514-12070523
22	GATA2	chr16:12069564-12069945	K562	blood:	n/a	n/a
23	POLR2A	chr16:12069686-12070825	HepG2	liver:	n/a	n/a
24	HEY1	chr16:12069658-12069894	K562	blood:	n/a	n/a
25	MYBL2	chr16:12069591-12070898	HepG2	liver:	n/a	n/a
26	FOSL2	chr16:12069582-12070066	SK-N-SH	brain:	n/a	n/a
27	KAP1	chr16:12069759-12070498	HEK293	kidney:	n/a	n/a
28	JUN	chr16:12069556-12069928	K562	blood:	n/a	n/a
29	MAX	chr16:12069663-12071152	Hela-S3	cervix:	n/a	chr16:12070760-12070770
30	POLR2A	chr16:12069594-12069998	HCT-116	colon:	n/a	n/a
31	TCF7L2	chr16:12069736-12070523	Hela-S3	cervix:	n/a	n/a
32	JUND	chr16:12069562-12069889	HepG2	liver:	n/a	chr16:12069729-12069740 chr16:12069682-12069693
33	CHD2	chr16:12069790-12070535	K562	blood:	n/a	n/a
34	CBX3	chr16:12069642-12069962	K562	blood:	n/a	n/a
35	EP300	chr16:12069595-12069853	K562	blood:	n/a	n/a
36	POLR2A	chr16:12069813-12071316	GM12892	blood:	n/a	n/a
37	MYC	chr16:12069604-12071182	K562	blood:	n/a	chr16:12070760-12070770
38	JUND	chr16:12069720-12069863	H1-hESC	embryonic stem cell:	n/a	chr16:12069729-12069740
39	POLR2A	chr16:12069784-12071528	GM18951	blood:	n/a	n/a
40	HCFC1	chr16:12069546-12071199	Hela-S3	cervix:	n/a	n/a
41	JUND	chr16:12069543-12070887	SK-N-SH	brain:	n/a	chr16:12069729-12069740 chr16:12070293-12070302 chr16:12069682-12069693 chr16:12070513-12070522
42	GATA3	chr16:12069408-12070131	SK-N-SH	brain:	n/a	n/a
43	RCOR1	chr16:12069788-12069848	HepG2	liver:	n/a	n/a
44	GABPA	chr16:12069720-12070847	A549	lung:	n/a	chr16:12070514-12070523
45	GATA3	chr16:12069625-12070083	MCF-7	breast:	n/a	n/a
46	RCOR1	chr16:12069687-12069845	K562	blood:	n/a	n/a
47	POLR2A	chr16:12069689-12070929	Hela-S3	cervix:	n/a	n/a
48	ZNF384	chr16:12069640-12069949	K562	blood:	n/a	n/a
49	RXRA	chr16:12069418-12070050	SK-N-SH	brain:	n/a	n/a
50	FOS	chr16:12069559-12069911	MCF10A-Er-Src	breast:	n/a	chr16:12069729-12069740 chr16:12069682-12069693

No.	Distal block	Cell Line	Cell type
1	chr16:12006809..12011472-chr16:12069677..12072698,7	MCF-7	breast:
2	chr16:12062509..12065114-chr16:12069207..12070961,2	MCF-7	breast:
3	chr16:12058363..12061770-chr16:12069205..12072370,4	MCF-7	breast:
4	chr16:12069629..12072468-chr16:12173207..12175470,2	MCF-7	breast:
5	chr16:12007711..12010113-chr16:12069770..12071913,2	MCF-7	breast:
6	chr16:12068975..12070484-chr16:12084406..12086978,2	K562	blood:
7	chr16:12068621..12072204-chr16:12129850..12134239,5	MCF-7	breast:
8	chr16:12006532..12011371-chr16:12068460..12073371,6	K562	blood:
9	chr12:57118643..57119257-chr16:12069612..12070224,2	Hela-S3	cervix:

Variant related genes	Relation type
SNX29	TF binding region
ENSG00000103342	Chromatin interaction
ENSG00000266163	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000241641	Chromatin interaction
ENSG00000048462	Chromatin interaction
ENSG00000048471	Chromatin interaction
ENSG00000260224	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs119090	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs370374	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs374146	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs375223	0.86[EUR][1000 genomes]
rs383972	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs386430	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs393313	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs393630	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs398700	0.88[EUR][1000 genomes]
rs399260	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs404854	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs415616	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs422527	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs428508	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs431580	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs434455	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs448756	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[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	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	nsv962195	chr16:12053526-12071576	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv3414588	chr16:12068301-12070249	Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12067600-12070000	Weak transcription	Aorta	Aorta
2	chr16:12069200-12070000	Flanking Active TSS	Dnd41	blood
3	chr16:12069400-12070000	Flanking Active TSS	K562	blood
4	chr16:12069400-12070200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr16:12069400-12070200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr16:12069400-12070200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr16:12069400-12070200	Flanking Active TSS	Fetal Brain Female	brain
8	chr16:12069400-12070200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr16:12069400-12070200	Flanking Active TSS	Hela-S3	cervix
10	chr16:12069400-12070400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr16:12069400-12070400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr16:12069400-12070400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr16:12069400-12071200	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr16:12069400-12071200	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr16:12069400-12071600	Active TSS	A549	lung
16	chr16:12069400-12072000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr16:12069400-12072200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr16:12069600-12070000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr16:12069600-12070000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr16:12069600-12070000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr16:12069600-12070000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr16:12069600-12070000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr16:12069600-12070000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr16:12069600-12070000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr16:12069600-12070000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr16:12069600-12070000	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr16:12069600-12070000	Flanking Active TSS	Brain Substantia Nigra	brain
28	chr16:12069600-12070000	Flanking Active TSS	Fetal Brain Male	brain
29	chr16:12069600-12070000	Flanking Active TSS	Ovary	ovary
30	chr16:12069600-12070000	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr16:12069600-12070000	Flanking Active TSS	Thymus	Thymus
32	chr16:12069600-12070000	Enhancers	Spleen	Spleen
33	chr16:12069600-12070000	Flanking Active TSS	HMEC	breast
34	chr16:12069600-12070000	Flanking Active TSS	NHDF-Ad	bronchial
35	chr16:12069600-12070200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr16:12069600-12070200	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr16:12069600-12070200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr16:12069600-12070200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr16:12069600-12070200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr16:12069600-12070200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr16:12069600-12070200	Flanking Active TSS	Liver	Liver
42	chr16:12069600-12070200	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr16:12069600-12070200	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr16:12069600-12070200	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr16:12069600-12070200	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr16:12069600-12070200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr16:12069600-12070200	Flanking Active TSS	Fetal Heart	heart
48	chr16:12069600-12070200	Flanking Active TSS	Fetal Lung	lung
49	chr16:12069600-12070200	Flanking Active TSS	Fetal Muscle Trunk	muscle
50	chr16:12069600-12070200	Flanking Active TSS	Fetal Muscle Leg	muscle

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