Variant report

Variant	rs1466382
Chromosome Location	chr12:57116834-57116835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57115901-57117242	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr12:57116688-57116909	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:57116738-57117339	U87	brain:	n/a	n/a
4	STAT3	chr12:57116788-57116868	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr12:57116295-57116919	GM12878	blood:	n/a	n/a
6	CHD1	chr12:57116778-57119555	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:57116545-57117501	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr12:57109094-57117058	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr12:57116385-57116910	PANC-1	pancreas:	n/a	n/a
10	STAT3	chr12:57116724-57116894	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT1	chr12:57116830-57116884	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:57116665-57119772	PFSK-1	brain:	n/a	n/a
13	MXI1	chr12:57116480-57120181	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr12:57116597-57117041	HepG2	liver:	n/a	n/a
15	POLR2A	chr12:57109356-57117115	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:57116533-57117033	K562	blood:	n/a	n/a
17	POLR2A	chr12:57116824-57116966	Hela-S3	cervix:	n/a	n/a
18	STAT3	chr12:57116789-57116868	MCF10A-Er-Src	breast:	n/a	n/a
19	MYC	chr12:57116774-57116994	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57075341..57085478-chr12:57112447..57121011,58	MCF-7	breast:
2	chr1:852957..855420-chr12:57116764..57119189,2	MCF-7	breast:
3	chr12:57115537..57117655-chr17:56707666..56710066,3	MCF-7	breast:
4	chr12:57116631..57120456-chr12:57479265..57482503,6	MCF-7	breast:
5	chr12:57026523..57033046-chr12:57115223..57120839,17	MCF-7	breast:
6	chr12:57091041..57092738-chr12:57114705..57116928,2	MCF-7	breast:
7	chr12:57035906..57041425-chr12:57115344..57122353,14	K562	blood:
8	chr12:57116832..57120019-chr12:57136517..57139167,4	K562	blood:
9	chr12:57038025..57041646-chr12:57113711..57120620,12	MCF-7	breast:
10	chr12:57074578..57085543-chr12:57108746..57121559,55	K562	blood:
11	chr12:57036857..57041663-chr12:57115375..57121628,17	MCF-7	breast:
12	chr12:57036938..57041843-chr12:57115310..57120529,12	K562	blood:
13	chr12:57076604..57085974-chr12:57112559..57120474,46	MCF-7	breast:
14	chr12:57078475..57085183-chr12:57112918..57121559,38	K562	blood:
15	chr12:57022951..57032187-chr12:57113330..57121462,17	K562	blood:
16	chr12:57115452..57117913-chr12:57483111..57485379,2	K562	blood:

No data

Variant related genes	Relation type
NACA	TF binding region
ENSG00000207031	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000223764	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000198056	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000110955	Chromatin interaction
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1026565	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10459246	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10747769	0.83[EUR][1000 genomes]
rs10747770	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783796	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876916	0.88[CEU][hapmap];0.93[CHB][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10876918	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1107479	0.94[ASW][hapmap];0.83[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.93[YRI][hapmap]
rs11171914	0.92[CHB][hapmap]
rs11171951	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171956	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171986	0.81[JPT][hapmap]
rs1131514	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12227117	0.82[ASN][1000 genomes]
rs12229457	0.93[CHB][hapmap]
rs12828563	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1563896	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs1563897	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1975875	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1979325	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2035081	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035082	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255074	0.83[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap]
rs2290893	0.83[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2290894	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926741	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2926743	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2926747	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2926748	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950387	0.80[CHB][hapmap]
rs2950390	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2958123	0.83[CEU][hapmap];0.93[CHB][hapmap]
rs2958127	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2958130	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958132	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958134	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2958148	0.88[CEU][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2958149	0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2958153	0.93[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs2958154	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2958155	1.00[ASW][hapmap];0.83[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes]
rs3214051	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.99[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4277148	0.81[JPT][hapmap]
rs4759254	0.93[CEU][hapmap];0.81[CHB][hapmap]
rs4759256	0.90[ASN][1000 genomes]
rs4788	0.96[ASN][1000 genomes]
rs4902	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137749	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7295862	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7297289	0.80[ASN][1000 genomes]
rs7303216	0.80[ASN][1000 genomes]
rs7313074	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7966391	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7967600	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7978685	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7980317	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7980835	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs898609	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898611	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs941207	0.86[CHB][hapmap]
rs9634246	0.93[CHB][hapmap];0.81[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1466382	RAB5B	cis	cerebellum	SCAN
rs1466382	HSD17B6	cis	cerebellum	SCAN
rs1466382	OR6C4	cis	cerebellum	SCAN
rs1466382	CELA1	cis	cerebellum	SCAN
rs1466382	STAT6	cis	parietal	SCAN
rs1466382	PRIM1	cis	cerebellum	SCAN
rs1466382	OR10A7	cis	parietal	SCAN
rs1466382	PRIM1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57108600-57117200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr12:57109600-57117000	Genic enhancers	Primary T cells fromperipheralblood	blood
3	chr12:57109600-57117000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
4	chr12:57109600-57117800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:57109800-57117200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr12:57110400-57117600	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr12:57112200-57117000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:57112200-57117200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:57113400-57117800	Transcr. at gene 5' and 3'	Hela-S3	cervix
10	chr12:57113600-57117000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
11	chr12:57113600-57118200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
12	chr12:57113800-57118800	Transcr. at gene 5' and 3'	K562	blood
13	chr12:57114200-57117600	Enhancers	Stomach Mucosa	stomach
14	chr12:57114400-57117000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:57114400-57117200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:57114400-57117400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:57114400-57118800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
18	chr12:57114400-57119200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:57114600-57118400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
20	chr12:57114800-57117600	Enhancers	Small Intestine	intestine
21	chr12:57114800-57117800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
22	chr12:57114800-57118000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
23	chr12:57114800-57118000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:57114800-57118800	Transcr. at gene 5' and 3'	Dnd41	blood
25	chr12:57115000-57117400	Transcr. at gene 5' and 3'	HepG2	liver
26	chr12:57115000-57117600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:57115000-57118000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
28	chr12:57115200-57117000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
29	chr12:57115200-57117600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:57115200-57117600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:57115200-57118000	Transcr. at gene 5' and 3'	NH-A	brain
32	chr12:57115200-57118200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
33	chr12:57115400-57117000	Transcr. at gene 5' and 3'	HUVEC	blood vessel
34	chr12:57115400-57117000	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
35	chr12:57115400-57117200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:57115400-57117400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
37	chr12:57115400-57117600	Weak transcription	Esophagus	oesophagus
38	chr12:57115400-57117800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
39	chr12:57115400-57118000	Transcr. at gene 5' and 3'	NHEK	skin
40	chr12:57115400-57118200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
41	chr12:57115400-57118600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:57115400-57118800	Transcr. at gene 5' and 3'	A549	lung
43	chr12:57115600-57117000	Transcr. at gene 5' and 3'	HSMM	muscle
44	chr12:57115600-57117400	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr12:57115600-57117600	Weak transcription	Lung	lung
46	chr12:57115600-57118200	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
47	chr12:57115800-57117000	Genic enhancers	Primary B cells from cord blood	blood
48	chr12:57115800-57117000	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
49	chr12:57115800-57117000	Enhancers	Placenta	Placenta
50	chr12:57115800-57117000	Transcr. at gene 5' and 3'	NHLF	lung

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