Variant report

Variant	rs1148555
Chromosome Location	chr12:57918634-57918635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57916882-57919110	U87	brain:	n/a	n/a
2	POLR2A	chr12:57915733-57918696	ECC-1	luminal epithelium:	n/a	n/a
3	NR2F2	chr12:57918172-57919041	K562	blood:	n/a	n/a
4	ZBTB7A	chr12:57918458-57919003	K562	blood:	n/a	n/a
5	POLR2A	chr12:57918554-57918642	HUVEC	blood vessel:	n/a	n/a
6	NR2F2	chr12:57918243-57918928	K562	blood:	n/a	n/a
7	POLR2A	chr12:57917814-57918735	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:57911713-57919299	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr12:57908382-57921207	K562	blood:	n/a	n/a
10	TEAD4	chr12:57918462-57919089	K562	blood:	n/a	n/a
11	POLR2A	chr12:57915375-57927219	K562	blood:	n/a	n/a
12	POLR2A	chr12:57912610-57921102	K562	blood:	n/a	n/a
13	POLR2A	chr12:57908062-57920927	K562	blood:	n/a	n/a
14	POLR2A	chr12:57917715-57918731	HL-60	blood:	n/a	n/a
15	TAL1	chr12:57918600-57918730	K562	blood:	n/a	n/a
16	RCOR1	chr12:57918505-57918897	K562	blood:	n/a	n/a
17	POLR2A	chr12:57917450-57919020	K562	blood:	n/a	n/a
18	POLR2A	chr12:57916870-57918716	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr12:57917867-57918679	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr12:57916888-57918820	U87	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57916512..57918954-chr12:58138893..58140769,2	MCF-7	breast:
2	chr12:57918214..57920020-chr12:58015895..58018076,2	MCF-7	breast:
3	chr12:57850154..57858218-chr12:57910899..57919538,20	K562	blood:
4	chr12:57916381..57918711-chr12:58131475..58134282,2	MCF-7	breast:
5	chr12:57889487..57901620-chr12:57907600..57919310,30	K562	blood:
6	chr12:57912818..57918945-chr12:58145879..58149998,6	MCF-7	breast:
7	chr12:57916409..57919050-chr12:57983099..57985919,3	MCF-7	breast:

No data

Variant related genes	Relation type
MBD6	TF binding region
DDIT3	TF binding region
ENSG00000135446	Chromatin interaction
ENSG00000139266	Chromatin interaction
ENSG00000135502	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000135439	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000111087	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1148552	0.81[LWK][hapmap]
rs1148553	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1148554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148556	0.90[LWK][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs1148557	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1284465	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1284605	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1299737	0.86[EUR][1000 genomes]
rs1629410	0.92[EUR][1000 genomes]
rs1669294	0.89[EUR][1000 genomes]
rs1669296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669297	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678537	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1679368	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1709871	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1709874	0.85[EUR][1000 genomes]
rs2127318	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2620677	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2620679	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]
rs2672571	0.92[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs2928382	0.85[EUR][1000 genomes]
rs2943696	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782129	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3847699	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs474544	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760273	0.83[EUR][1000 genomes]
rs496245	0.92[CEU][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs508904	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs511752	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs542278	0.91[ASW][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs697221	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703835	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs703836	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs703837	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs703838	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs703839	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7299631	0.95[EUR][1000 genomes]
rs747340	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs775236	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775237	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775241	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs775323	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs775324	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs776038	0.92[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs776039	0.86[EUR][1000 genomes]
rs7964074	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs796546	0.87[EUR][1000 genomes]
rs7969683	0.82[EUR][1000 genomes]
rs899653	0.95[CHD][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs9737891	0.88[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1148555	KRT81	cis	parietal	SCAN
rs1148555	DCTN2	cis	Muscle Skeletal	GTEx
rs1148555	ATF7	cis	cerebellum	SCAN
rs1148555	AVIL	cis	cerebellum	SCAN
rs1148555	ACVRL1	cis	cerebellum	SCAN
rs1148555	KRT7	cis	cerebellum	SCAN
rs1148555	CALCOCO1	cis	cerebellum	SCAN
rs1148555	ITGB7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57917000-57919000	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr12:57917200-57919000	Flanking Active TSS	Brain Anterior Caudate	brain
3	chr12:57917200-57920800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:57917400-57918800	Transcr. at gene 5' and 3'	K562	blood
5	chr12:57917400-57922800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:57917600-57918800	Flanking Active TSS	Psoas Muscle	Psoas
7	chr12:57917600-57918800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
8	chr12:57917600-57919000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr12:57917600-57920400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:57917600-57921000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:57917600-57939600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:57917800-57918800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:57917800-57918800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:57917800-57918800	Genic enhancers	Fetal Lung	lung
15	chr12:57917800-57918800	Transcr. at gene 5' and 3'	HSMM	muscle
16	chr12:57917800-57919000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr12:57917800-57919000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:57917800-57919000	Genic enhancers	Colonic Mucosa	Colon
19	chr12:57917800-57919000	Genic enhancers	Pancreas	Pancrea
20	chr12:57917800-57919000	Enhancers	Right Atrium	heart
21	chr12:57917800-57919000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
22	chr12:57917800-57919000	Genic enhancers	Spleen	Spleen
23	chr12:57917800-57919200	Genic enhancers	Primary B cells from peripheral blood	blood
24	chr12:57917800-57919200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr12:57917800-57919400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:57917800-57919600	Genic enhancers	Left Ventricle	heart
27	chr12:57917800-57920200	Enhancers	Fetal Brain Male	brain
28	chr12:57917800-57920600	Genic enhancers	Primary T cells fromperipheralblood	blood
29	chr12:57917800-57920800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:57917800-57921400	Genic enhancers	Fetal Muscle Trunk	muscle
31	chr12:57917800-57922400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr12:57918000-57918800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:57918000-57918800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:57918000-57919000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:57918000-57919000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
36	chr12:57918000-57919000	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:57918000-57919000	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
38	chr12:57918000-57919000	Enhancers	HUVEC	blood vessel
39	chr12:57918000-57919200	Genic enhancers	Colon Smooth Muscle	Colon
40	chr12:57918000-57919200	Genic enhancers	Rectal Mucosa Donor 31	rectum
41	chr12:57918000-57919400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:57918000-57919400	Genic enhancers	Primary monocytes fromperipheralblood	blood
43	chr12:57918000-57919400	Genic enhancers	Fetal Stomach	stomach
44	chr12:57918000-57919400	Genic enhancers	Rectal Mucosa Donor 29	rectum
45	chr12:57918000-57919600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:57918000-57919800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:57918000-57919800	Genic enhancers	Right Ventricle	heart
48	chr12:57918000-57920000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:57918000-57920000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
50	chr12:57918000-57920200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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