Variant report

Variant	rs2620679
Chromosome Location	chr12:57922363-57922364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57921267-57922558	K562	blood:	n/a	n/a
2	POLR2A	chr12:57921012-57924882	K562	blood:	n/a	n/a
3	POLR2A	chr12:57920560-57922594	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr12:57922341-57922877	K562	blood:	n/a	n/a
5	POLR2A	chr12:57922101-57922548	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr12:57922112-57922734	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:57922141-57923223	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr12:57922194-57922536	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr12:57921920-57922515	K562	blood:	n/a	n/a
10	POLR2A	chr12:57915375-57927219	K562	blood:	n/a	n/a
11	POLR2A	chr12:57922303-57922517	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr12:57922130-57923138	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr12:57922077-57923193	U87	brain:	n/a	n/a
14	POLR2A	chr12:57922101-57923092	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr12:57921936-57922522	A549	lung:	n/a	n/a
16	POLR2A	chr12:57921504-57923901	K562	blood:	n/a	n/a
17	POLR2A	chr12:57921450-57922522	U87	brain:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57921185..57924132-chr12:58144470..58146639,2	MCF-7	breast:
2	chr12:57919943..57923943-chr12:57984305..57987540,4	MCF-7	breast:

No data

Variant related genes	Relation type
MBD6	TF binding region
ENSG00000135446	Chromatin interaction
ENSG00000166908	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1148553	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1148554	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1148555	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1148557	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1284465	0.87[EUR][1000 genomes]
rs1284605	0.85[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1299737	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1629410	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1669294	0.84[EUR][1000 genomes]
rs1669296	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669297	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1678537	0.92[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs1679368	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1709871	0.85[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.88[EUR][1000 genomes]
rs1709874	0.83[EUR][1000 genomes]
rs2127318	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2620677	0.83[EUR][1000 genomes]
rs2672571	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap]
rs2928382	0.83[EUR][1000 genomes]
rs2943696	0.84[EUR][1000 genomes]
rs3782129	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825080	0.89[JPT][hapmap]
rs3847699	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs474544	0.84[EUR][1000 genomes]
rs4760273	0.80[EUR][1000 genomes]
rs496245	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs511752	0.92[CEU][hapmap];0.89[YRI][hapmap]
rs542278	0.91[GIH][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap]
rs697221	0.92[ASW][hapmap];0.92[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs703835	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs703836	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs703837	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs703838	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs703839	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7299631	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs747340	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs775236	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs775237	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs775241	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs775323	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs775324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs776038	0.92[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs776039	0.84[EUR][1000 genomes]
rs7964074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs796546	0.84[EUR][1000 genomes]
rs899653	0.82[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.96[TSI][hapmap]
rs9737891	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
8	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
9	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
10	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
11	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
12	nsv1053930	chr12:57921188-57969659	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	n/a

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2620679	DCTN2	cis	Muscle Skeletal	GTEx
rs2620679	ACVRL1	cis	cerebellum	SCAN
rs2620679	KRT81	cis	parietal	SCAN
rs2620679	AVIL	cis	cerebellum	SCAN
rs2620679	ATF7	cis	cerebellum	SCAN
rs2620679	CALCOCO1	cis	cerebellum	SCAN
rs2620679	ITGB7	cis	cerebellum	SCAN
rs2620679	KRT7	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57917400-57922800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:57917600-57939600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:57917800-57922400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:57918000-57924000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:57918400-57929400	Strong transcription	Ovary	ovary
6	chr12:57918400-57929800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:57918600-57923400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:57918600-57924400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:57918600-57925400	Weak transcription	Fetal Kidney	kidney
10	chr12:57918600-57925400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:57918600-57929000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:57918600-57929600	Strong transcription	Aorta	Aorta
13	chr12:57918600-57929600	Strong transcription	Rectal Smooth Muscle	rectum
14	chr12:57918600-57930400	Strong transcription	Lung	lung
15	chr12:57918600-57933600	Strong transcription	Brain Hippocampus Middle	brain
16	chr12:57918600-57934800	Strong transcription	Osteobl	bone
17	chr12:57918600-57936400	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr12:57918600-57939600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:57918800-57922800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:57918800-57923800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:57918800-57929000	Strong transcription	Small Intestine	intestine
22	chr12:57918800-57929400	Strong transcription	Gastric	stomach
23	chr12:57918800-57929600	Strong transcription	Brain Substantia Nigra	brain
24	chr12:57918800-57929600	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr12:57918800-57929800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:57918800-57929800	Strong transcription	Fetal Lung	lung
27	chr12:57918800-57930600	Strong transcription	Primary T cells from cord blood	blood
28	chr12:57918800-57933800	Strong transcription	NHEK	skin
29	chr12:57919000-57922400	Weak transcription	NHDF-Ad	bronchial
30	chr12:57919000-57922800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr12:57919000-57924000	Weak transcription	Fetal Heart	heart
32	chr12:57919000-57928800	Strong transcription	Colonic Mucosa	Colon
33	chr12:57919000-57929400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr12:57919000-57929400	Strong transcription	Esophagus	oesophagus
35	chr12:57919000-57929600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr12:57919000-57929600	Strong transcription	Liver	Liver
37	chr12:57919000-57929600	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:57919000-57929800	Strong transcription	Spleen	Spleen
39	chr12:57919000-57930000	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr12:57919000-57930000	Strong transcription	NHLF	lung
41	chr12:57919000-57931200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:57919000-57932000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:57919000-57935600	Strong transcription	Thymus	Thymus
44	chr12:57919000-57937400	Weak transcription	Right Atrium	heart
45	chr12:57919200-57928800	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr12:57919200-57929000	Strong transcription	GM12878-XiMat	blood
47	chr12:57919200-57929800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr12:57919200-57934800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:57919200-57939600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:57919400-57922400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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