Variant report

Variant	rs1284465
Chromosome Location	chr12:57904170-57904171
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	FOS	chr12:57903768-57904173	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr12:57903786-57904170	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr12:57903800-57904173	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr12:57903906-57904189	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57883464..57886138-chr12:57902032..57904531,3	K562	blood:
2	chr12:57896366..57901111-chr12:57901647..57907518,8	K562	blood:
3	chr12:57881369..57883611-chr12:57902104..57905410,4	MCF-7	breast:
4	chr12:57901367..57904332-chr12:57904666..57906623,2	K562	blood:

Variant related genes	Relation type
RNU6-594P	TF binding region
MARS	TF binding region
RN7SL312P	TF binding region
ENSG00000123329	Chromatin interaction
ENSG00000252865	Chromatin interaction
ENSG00000166986	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1148553	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1148554	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1148555	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1148557	0.92[EUR][1000 genomes]
rs1284605	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1284606	0.85[AMR][1000 genomes]
rs1299737	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1629410	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669294	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1669296	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1669297	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678537	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1709871	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1709874	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2127318	0.90[EUR][1000 genomes]
rs2620677	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2620679	0.87[EUR][1000 genomes]
rs2672571	0.80[AMR][1000 genomes]
rs2673326	0.83[AMR][1000 genomes]
rs2928382	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2943696	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3782129	0.86[EUR][1000 genomes]
rs3847699	0.91[EUR][1000 genomes]
rs472895	0.88[AMR][1000 genomes]
rs474544	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4760273	0.87[EUR][1000 genomes]
rs496245	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs508904	0.86[AMR][1000 genomes]
rs511752	0.85[AMR][1000 genomes]
rs542278	0.84[AMR][1000 genomes]
rs569251	0.88[AMR][1000 genomes]
rs697221	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs703835	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs703836	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs703837	0.87[EUR][1000 genomes]
rs703838	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs703839	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7299631	0.86[EUR][1000 genomes]
rs747340	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs775236	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs775237	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs775241	0.87[EUR][1000 genomes]
rs775323	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs775324	0.87[EUR][1000 genomes]
rs776038	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs776039	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7964074	0.85[EUR][1000 genomes]
rs796546	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7969683	0.87[EUR][1000 genomes]
rs9737891	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv899120	chr12:57886609-57921188	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1284465	DCTN2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57882800-57905800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:57883000-57910600	Weak transcription	Right Atrium	heart
3	chr12:57883200-57911200	Strong transcription	Fetal Intestine Small	intestine
4	chr12:57885600-57911200	Weak transcription	Fetal Heart	heart
5	chr12:57888600-57912200	Strong transcription	Fetal Stomach	stomach
6	chr12:57892800-57908600	Weak transcription	Stomach Mucosa	stomach
7	chr12:57896200-57905400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:57896200-57905600	Weak transcription	NHDF-Ad	bronchial
9	chr12:57899000-57905200	Weak transcription	NHLF	lung
10	chr12:57899200-57905000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:57899600-57906400	Weak transcription	Small Intestine	intestine
12	chr12:57900000-57904600	Weak transcription	Right Ventricle	heart
13	chr12:57900000-57905000	Weak transcription	Gastric	stomach
14	chr12:57900000-57905200	Weak transcription	Colonic Mucosa	Colon
15	chr12:57900200-57905000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:57900200-57905600	Weak transcription	Esophagus	oesophagus
17	chr12:57900400-57904200	Weak transcription	Brain Anterior Caudate	brain
18	chr12:57900400-57904600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:57900400-57905000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:57900400-57905400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:57900400-57905400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:57900400-57905400	Weak transcription	Ovary	ovary
23	chr12:57900400-57905600	Weak transcription	Fetal Brain Male	brain
24	chr12:57900600-57904400	Weak transcription	Spleen	Spleen
25	chr12:57900600-57904800	Weak transcription	Aorta	Aorta
26	chr12:57900600-57905000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr12:57900600-57905000	Weak transcription	Left Ventricle	heart
28	chr12:57900600-57905000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr12:57900600-57905000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:57900600-57905200	Weak transcription	Brain Angular Gyrus	brain
31	chr12:57900600-57905200	Weak transcription	Brain Substantia Nigra	brain
32	chr12:57900600-57905200	Weak transcription	Fetal Kidney	kidney
33	chr12:57900600-57905400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr12:57900600-57905800	Weak transcription	Psoas Muscle	Psoas
35	chr12:57900600-57912000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr12:57900600-57912800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:57901600-57910600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:57901600-57911000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:57901600-57911800	Strong transcription	Lung	lung
40	chr12:57901800-57906800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:57901800-57911600	Strong transcription	Thymus	Thymus
42	chr12:57901800-57911800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr12:57901800-57911800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr12:57902000-57912400	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr12:57902200-57909800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:57902200-57910000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:57902200-57910600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:57902200-57911600	Strong transcription	Fetal Muscle Leg	muscle
49	chr12:57902200-57912000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:57902200-57912000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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