Variant report

Variant	rs1629410
Chromosome Location	chr12:57902253-57902254
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr12:57902220-57902385	GM12892	blood:	n/a	n/a
2	PAX5	chr12:57902187-57902372	GM12878	blood:	n/a	n/a
3	PAX5	chr12:57902129-57902398	GM12878	blood:	n/a	n/a
4	PAX5	chr12:57902137-57902448	GM12878	blood:	n/a	n/a
5	PAX5	chr12:57902092-57902619	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

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:

No data

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

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1148553	0.86[EUR][1000 genomes]
rs1148554	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1148555	0.92[EUR][1000 genomes]
rs1148557	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1284465	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1284605	0.91[EUR][1000 genomes]
rs1284606	0.91[AMR][1000 genomes]
rs1299737	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1617196	0.80[AMR][1000 genomes]
rs1669294	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1669296	0.88[EUR][1000 genomes]
rs1669297	0.88[EUR][1000 genomes]
rs1678537	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1709871	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1709874	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2127318	0.90[EUR][1000 genomes]
rs2620677	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2620679	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2672571	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2673326	0.89[AMR][1000 genomes]
rs2928382	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2943696	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3782129	0.87[EUR][1000 genomes]
rs3847699	0.92[EUR][1000 genomes]
rs472895	0.87[AMR][1000 genomes]
rs474544	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4760273	0.88[EUR][1000 genomes]
rs496245	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs508904	0.85[AMR][1000 genomes]
rs511752	0.91[AMR][1000 genomes]
rs541869	0.85[AMR][1000 genomes]
rs542278	0.82[AMR][1000 genomes]
rs569251	0.87[AMR][1000 genomes]
rs697221	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs703835	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs703836	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs703837	0.88[EUR][1000 genomes]
rs703838	0.87[EUR][1000 genomes]
rs703839	0.86[EUR][1000 genomes]
rs7299631	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs747340	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs775236	0.88[EUR][1000 genomes]
rs775237	0.88[EUR][1000 genomes]
rs775241	0.88[EUR][1000 genomes]
rs775323	0.88[EUR][1000 genomes]
rs775324	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs776038	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs776039	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7964074	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs796546	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7969683	0.88[EUR][1000 genomes]
rs9737891	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][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
rs1629410	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	chr12:57883200-57902400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:57883200-57911200	Strong transcription	Fetal Intestine Small	intestine
5	chr12:57883400-57903000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:57884000-57902400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:57884000-57903200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:57885600-57911200	Weak transcription	Fetal Heart	heart
9	chr12:57888600-57912200	Strong transcription	Fetal Stomach	stomach
10	chr12:57892800-57908600	Weak transcription	Stomach Mucosa	stomach
11	chr12:57896200-57905400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:57896200-57905600	Weak transcription	NHDF-Ad	bronchial
13	chr12:57898200-57902800	Weak transcription	Hela-S3	cervix
14	chr12:57899000-57905200	Weak transcription	NHLF	lung
15	chr12:57899200-57905000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:57899600-57906400	Weak transcription	Small Intestine	intestine
17	chr12:57899800-57903000	Weak transcription	HUVEC	blood vessel
18	chr12:57900000-57904600	Weak transcription	Right Ventricle	heart
19	chr12:57900000-57905000	Weak transcription	Gastric	stomach
20	chr12:57900000-57905200	Weak transcription	Colonic Mucosa	Colon
21	chr12:57900200-57902400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:57900200-57902600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:57900200-57902600	Weak transcription	HepG2	liver
24	chr12:57900200-57904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:57900200-57905000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:57900200-57905600	Weak transcription	Esophagus	oesophagus
27	chr12:57900400-57902400	Weak transcription	Primary B cells from cord blood	blood
28	chr12:57900400-57902400	Weak transcription	Fetal Brain Female	brain
29	chr12:57900400-57902600	Weak transcription	Adipose Nuclei	Adipose
30	chr12:57900400-57902800	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:57900400-57903000	Weak transcription	Primary T cells from cord blood	blood
32	chr12:57900400-57903000	Weak transcription	Fetal Intestine Large	intestine
33	chr12:57900400-57904000	Weak transcription	Pancreas	Pancrea
34	chr12:57900400-57904200	Weak transcription	Brain Anterior Caudate	brain
35	chr12:57900400-57904600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr12:57900400-57905000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr12:57900400-57905400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr12:57900400-57905400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:57900400-57905400	Weak transcription	Ovary	ovary
40	chr12:57900400-57905600	Weak transcription	Fetal Brain Male	brain
41	chr12:57900600-57902400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:57900600-57902400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:57900600-57902400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr12:57900600-57902400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:57900600-57902400	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:57900600-57902400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr12:57900600-57902400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr12:57900600-57902400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:57900600-57902400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:57900600-57902400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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