Variant report

Variant	rs496245
Chromosome Location	chr12:57891496-57891497
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57890580-57891874	GM12891	blood:	n/a	n/a
2	POLR2A	chr12:57889904-57892774	K562	blood:	n/a	n/a
3	POLR2A	chr12:57890313-57891529	K562	blood:	n/a	n/a
4	POLR2A	chr12:57890395-57892794	K562	blood:	n/a	n/a
5	POLR2A	chr12:57890477-57892526	GM12892	blood:	n/a	n/a
6	POLR2A	chr12:57891176-57892622	K562	blood:	n/a	n/a
7	POLR2A	chr12:57890599-57891823	K562	blood:	n/a	n/a
8	POLR2A	chr12:57890437-57892735	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr12:57890471-57892478	GM12892	blood:	n/a	n/a
10	POLR2A	chr12:57890570-57892640	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:57889953-57892706	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr12:57890418-57892599	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr12:57891127-57891769	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:57890913-57891585	U87	brain:	n/a	n/a
15	POLR2A	chr12:57891046-57892062	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr12:57890533-57892535	GM12892	blood:	n/a	n/a
17	POLR2A	chr12:57890507-57892027	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:57890586-57892499	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr12:57890304-57892457	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr12:57891069-57891585	HCT-116	colon:	n/a	n/a
21	POLR2A	chr12:57890566-57892015	A549	lung:	n/a	n/a
22	POLR2A	chr12:57890400-57892251	U87	brain:	n/a	n/a
23	POLR2A	chr12:57891060-57892609	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr12:57890062-57892944	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr12:57890406-57892773	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:57891094-57892090	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:57890865-57891585	U87	brain:	n/a	n/a
28	POLR2A	chr12:57890987-57892467	HL-60	blood:	n/a	n/a
29	POLR2A	chr12:57889520-57892784	HepG2	liver:	n/a	n/a
30	POLR2A	chr12:57890702-57892319	GM12891	blood:	n/a	n/a
31	POLR2A	chr12:57891213-57891582	MCF-7	breast:	n/a	n/a
32	POLR2A	chr12:57891484-57891666	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:57890347-57892709	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr12:57891102-57891506	H1-hESC	embryonic stem cell:	n/a	n/a
35	SPI1	chr12:57891232-57891866	HL-60	blood:	n/a	chr12:57891420-57891433 chr12:57891422-57891431 chr12:57891426-57891435
36	POLR2A	chr12:57890328-57891934	GM12891	blood:	n/a	n/a
37	POLR2A	chr12:57890574-57892017	GM12891	blood:	n/a	n/a
38	POLR2A	chr12:57889712-57892735	K562	blood:	n/a	n/a
39	POLR2A	chr12:57890452-57892223	U87	brain:	n/a	n/a
40	POLR2A	chr12:57891005-57891514	HCT-116	colon:	n/a	n/a
41	POLR2A	chr12:57890527-57891793	SK-N-SH	brain:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57851548..57854226-chr12:57891016..57893110,2	K562	blood:
2	chr12:57883133..57885464-chr12:57889666..57892523,2	MCF-7	breast:
3	chr12:57880706..57883916-chr12:57890365..57893434,6	MCF-7	breast:
4	chr12:57890344..57892939-chr12:57904796..57907275,3	K562	blood:
5	chr12:57890654..57892661-chr12:57903165..57906140,2	MCF-7	breast:
6	chr12:57889408..57891774-chr12:58150990..58153331,2	K562	blood:
7	chr12:57890108..57896575-chr12:57912675..57917509,9	MCF-7	breast:
8	chr12:57889187..57891689-chr12:57896178..57899261,4	K562	blood:
9	chr12:57889701..57892074-chr12:57903577..57905804,2	MCF-7	breast:
10	chr12:57889716..57891689-chr12:57897761..57899906,2	K562	blood:
11	chr12:57889613..57892286-chr12:57893437..57895959,2	MCF-7	breast:
12	chr12:57890573..57894514-chr12:57912146..57915649,5	MCF-7	breast:
13	chr12:57853841..57856482-chr12:57889297..57892224,2	K562	blood:
14	chr12:57889753..57892450-chr12:57908633..57910500,2	MCF-7	breast:
15	chr12:57889487..57901620-chr12:57907600..57919310,30	K562	blood:

No data

Variant related genes	Relation type
MARS	TF binding region
ENSG00000123329	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000252865	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000139266	Chromatin interaction
ENSG00000264046	Chromatin interaction
ENSG00000166986	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1148553	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1148554	0.92[CEU][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1148555	0.92[CEU][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1148557	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs1284465	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1284605	0.92[CEU][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1284606	0.87[AMR][1000 genomes]
rs1299737	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1629410	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1669294	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669296	0.92[CEU][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1669297	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1678537	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1709871	1.00[CEU][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1709874	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2127318	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2620677	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2620679	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2672571	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs2673326	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2928382	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2943696	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782129	0.84[EUR][1000 genomes]
rs3847699	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs472895	0.91[AMR][1000 genomes]
rs474544	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760273	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs508904	0.83[CEU][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs511752	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs542278	0.83[CEU][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes]
rs569251	0.91[AMR][1000 genomes]
rs697221	0.85[CEU][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs703835	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs703836	0.90[EUR][1000 genomes]
rs703837	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs703838	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs703839	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7299631	0.84[EUR][1000 genomes]
rs747340	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs775236	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs775237	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs775241	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs775323	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs775324	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs776038	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs776039	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7964074	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs796546	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7969683	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs899653	0.83[CEU][hapmap]
rs9737891	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][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	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
15	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
16	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
rs496245	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	chr12:57883200-57893600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:57883200-57900600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:57883200-57900600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr12:57883200-57900800	Strong transcription	Thymus	Thymus
7	chr12:57883200-57902400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:57883200-57911200	Strong transcription	Fetal Intestine Small	intestine
9	chr12:57883400-57900600	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr12:57883400-57900600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:57883400-57900600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:57883400-57900600	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:57883400-57900600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:57883400-57900600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:57883400-57900800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:57883400-57903000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:57883800-57899800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:57884000-57900600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:57884000-57900600	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:57884000-57902400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:57884000-57903200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:57884400-57894000	Weak transcription	Psoas Muscle	Psoas
23	chr12:57884400-57900800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:57885600-57891800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr12:57885600-57893800	Weak transcription	Small Intestine	intestine
26	chr12:57885600-57911200	Weak transcription	Fetal Heart	heart
27	chr12:57885800-57891800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:57885800-57893600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:57886800-57891600	Weak transcription	Brain Angular Gyrus	brain
30	chr12:57886800-57891800	Weak transcription	Pancreas	Pancrea
31	chr12:57887000-57891600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:57887000-57891800	Weak transcription	Esophagus	oesophagus
33	chr12:57887000-57892000	Weak transcription	Stomach Mucosa	stomach
34	chr12:57887000-57892000	Weak transcription	NHDF-Ad	bronchial
35	chr12:57887000-57892200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:57887200-57900600	Strong transcription	Dnd41	blood
37	chr12:57887800-57899600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:57887800-57900600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:57887800-57900600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:57888000-57900600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr12:57888000-57900600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:57888000-57900600	Strong transcription	Fetal Muscle Leg	muscle
43	chr12:57888400-57894000	Strong transcription	Lung	lung
44	chr12:57888600-57893000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:57888600-57912200	Strong transcription	Fetal Stomach	stomach
46	chr12:57888800-57897800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:57888800-57900600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:57888800-57900600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr12:57888800-57900600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:57889200-57892600	Strong transcription	Right Ventricle	heart

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