Variant report

Variant	rs1284606
Chromosome Location	chr12:57881363-57881364
allele	A/G
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	POLR2A	chr12:57881333-57882267	GM12892	blood:	n/a	n/a
2	TCF12	chr12:57881276-57882206	ECC-1	luminal epithelium:	n/a	n/a
3	SP1	chr12:57881359-57882140	A549	lung:	n/a	chr12:57882015-57882027 chr12:57882012-57882026 chr12:57882017-57882026 chr12:57882015-57882027 chr12:57882016-57882025
4	CBX3	chr12:57881297-57882049	K562	blood:	n/a	n/a
5	CTCF	chr12:57881050-57882049	SK-N-SH	brain:	n/a	n/a
6	TAF1	chr12:57881329-57882541	ECC-1	luminal epithelium:	n/a	n/a
7	FOXM1	chr12:57881319-57881940	GM12878	blood:	n/a	n/a
8	ZNF384	chr12:57881200-57882019	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:57881287-57882236	HUVEC	blood vessel:	n/a	n/a
10	MAX	chr12:57881319-57882296	HCT-116	colon:	n/a	chr12:57881847-57881856
11	MAX	chr12:57881084-57882844	ECC-1	luminal epithelium:	n/a	chr12:57881847-57881856
12	POLR2A	chr12:57881352-57882717	PFSK-1	brain:	n/a	n/a
13	SREBP1	chr12:57881246-57882746	GM12878	blood:	n/a	chr12:57882227-57882238
14	GABPA	chr12:57881306-57882441	A549	lung:	n/a	n/a
15	GABPA	chr12:57881289-57882313	A549	lung:	n/a	n/a
16	NR2F2	chr12:57881105-57882048	K562	blood:	n/a	n/a
17	MXI1	chr12:57881206-57883423	IMR90	lung:	n/a	n/a
18	MAX	chr12:57881206-57882448	K562	blood:	n/a	chr12:57881847-57881856
19	JUN	chr12:57881281-57883804	K562	blood:	n/a	chr12:57882014-57882023 chr12:57882152-57882161 chr12:57883182-57883190 chr12:57882015-57882024
20	TCF12	chr12:57881251-57882255	A549	lung:	n/a	n/a
21	MAX	chr12:57881332-57882378	A549	lung:	n/a	chr12:57881847-57881856
22	PAX5	chr12:57881323-57881985	GM12878	blood:	n/a	n/a
23	HCFC1	chr12:57880939-57883243	Hela-S3	cervix:	n/a	n/a
24	TRIM28	chr12:57881334-57882052	K562	blood:	n/a	n/a
25	GABPA	chr12:57881074-57882501	MCF-7	breast:	n/a	n/a
26	BCL3	chr12:57881010-57882220	A549	lung:	n/a	chr12:57882150-57882159
27	SP1	chr12:57881353-57882088	A549	lung:	n/a	chr12:57882015-57882027 chr12:57882012-57882026 chr12:57882017-57882026 chr12:57882015-57882027 chr12:57882016-57882025
28	SIX5	chr12:57881235-57882247	A549	lung:	n/a	chr12:57881783-57881797
29	ETS1	chr12:57881306-57882269	A549	lung:	n/a	chr12:57881783-57881796 chr12:57881839-57881848
30	MXI1	chr12:57880974-57883175	SK-N-SH	brain:	n/a	n/a
31	TCF12	chr12:57881301-57882223	ECC-1	luminal epithelium:	n/a	n/a
32	KAP1	chr12:57881279-57882046	HEK293	kidney:	n/a	n/a
33	ZNF384	chr12:57881084-57882017	K562	blood:	n/a	n/a
34	MAX	chr12:57881229-57882300	HCT-116	colon:	n/a	chr12:57881847-57881856
35	ZNF143	chr12:57881152-57882139	K562	blood:	n/a	chr12:57881720-57881735 chr12:57881785-57881803 chr12:57881719-57881738
36	RCOR1	chr12:57881123-57883656	IMR90	lung:	n/a	n/a
37	POLR2A	chr12:57881336-57882211	HUVEC	blood vessel:	n/a	n/a
38	SP2	chr12:57881326-57882029	HepG2	liver:	n/a	n/a
39	ELF1	chr12:57881302-57882151	GM12878	blood:	n/a	chr12:57881807-57881819
40	SP2	chr12:57881330-57882066	HepG2	liver:	n/a	n/a
41	PAX5	chr12:57881324-57881882	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57879869..57888452-chr12:57905809..57918310,36	K562	blood:
2	chr12:57872773..57878513-chr12:57879040..57886839,8	K562	blood:
3	chr12:57866650..57869717-chr12:57880833..57883787,3	MCF-7	breast:
4	chr12:57880356..57884964-chr12:57910434..57915758,10	MCF-7	breast:
5	chr12:57880552..57883318-chr12:57915762..57917586,2	MCF-7	breast:
6	chr12:57880789..57883714-chr12:57919502..57921245,2	K562	blood:
7	chr12:57855324..57857821-chr12:57881155..57883248,2	MCF-7	breast:
8	chr12:57881044..57886958-chr12:57910925..57918058,16	MCF-7	breast:
9	chr12:57824473..57826346-chr12:57880233..57882392,2	MCF-7	breast:
10	chr12:57869556..57871935-chr12:57881103..57884583,3	K562	blood:
11	chr12:57848182..57850484-chr12:57880307..57884604,3	K562	blood:
12	chr12:57879207..57888227-chr12:57906247..57918451,36	K562	blood:

Variant related genes	Relation type
MARS	TF binding region
ENSG00000258001	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000264046	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000139269	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000179912	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1148557	0.81[AMR][1000 genomes]
rs1284465	0.85[AMR][1000 genomes]
rs1299737	0.91[AMR][1000 genomes]
rs1617196	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1629410	0.91[AMR][1000 genomes]
rs1669294	0.85[AMR][1000 genomes]
rs1678537	0.85[AMR][1000 genomes]
rs1709871	0.91[AMR][1000 genomes]
rs1709874	0.89[AMR][1000 genomes]
rs2620677	0.89[AMR][1000 genomes]
rs2672571	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2673326	0.89[AMR][1000 genomes]
rs2928382	0.85[AMR][1000 genomes]
rs2943696	0.87[AMR][1000 genomes]
rs472895	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs474544	0.85[AMR][1000 genomes]
rs496245	0.87[AMR][1000 genomes]
rs508904	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs511752	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs539244	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs541869	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs542278	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs569251	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs697221	0.81[AMR][1000 genomes]
rs703835	0.83[AMR][1000 genomes]
rs703836	0.83[AMR][1000 genomes]
rs747340	0.91[AMR][1000 genomes]
rs776038	0.89[AMR][1000 genomes]
rs776039	0.89[AMR][1000 genomes]
rs796546	0.91[AMR][1000 genomes]
rs899653	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9737891	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak 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	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers 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	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers 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 miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
14	nsv819781	chr12:57873564-57882217	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a
15	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
16	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers 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	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1284606	DCTN2	cis	Muscle Skeletal	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57875800-57881400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr12:57877400-57881400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr12:57877600-57881400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:57877600-57881400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:57877600-57881400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:57877600-57881800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:57877800-57881400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:57881000-57881400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:57881000-57881400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr12:57881000-57881400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:57881000-57881400	Flanking Active TSS	A549	lung
12	chr12:57881000-57881400	Flanking Active TSS	HSMMtube	muscle
13	chr12:57881000-57881400	Flanking Active TSS	K562	blood
14	chr12:57881000-57881600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:57881000-57881600	Enhancers	Primary B cells from peripheral blood	blood
16	chr12:57881000-57881600	Enhancers	Primary T cells fromperipheralblood	blood
17	chr12:57881000-57881600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr12:57881000-57881600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:57881000-57881600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr12:57881000-57881600	Flanking Active TSS	Dnd41	blood
21	chr12:57881000-57881800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr12:57881000-57881800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:57881000-57881800	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr12:57881000-57882200	Active TSS	Stomach Smooth Muscle	stomach
25	chr12:57881000-57882400	Active TSS	Colon Smooth Muscle	Colon
26	chr12:57881000-57882400	Active TSS	Fetal Lung	lung
27	chr12:57881000-57882800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:57881200-57881400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:57881200-57881400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:57881200-57881400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:57881200-57881400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr12:57881200-57881400	Enhancers	Primary B cells from cord blood	blood
33	chr12:57881200-57881400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr12:57881200-57881400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:57881200-57881400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr12:57881200-57881400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:57881200-57881400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:57881200-57881400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:57881200-57881400	Enhancers	Liver	Liver
40	chr12:57881200-57881400	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr12:57881200-57881400	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr12:57881200-57881400	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr12:57881200-57881400	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr12:57881200-57881400	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr12:57881200-57881400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
46	chr12:57881200-57881400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:57881200-57881400	Flanking Active TSS	Brain Substantia Nigra	brain
48	chr12:57881200-57881400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr12:57881200-57881400	Flanking Active TSS	Esophagus	oesophagus
50	chr12:57881200-57881400	Flanking Active TSS	Fetal Brain Female	brain

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