Variant report

Variant	rs2732466
Chromosome Location	chr12:48732459-48732460
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:48732435-48732669	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:48731676-48734156	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr12:48731856-48734187	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48730358..48732811-chr12:48836328..48838155,2	MCF-7	breast:
2	chr12:48732035..48733570-chr12:48734227..48737131,2	MCF-7	breast:
3	chr12:48731724..48737573-chr12:48737990..48746470,14	K562	blood:
4	chr12:48729428..48731486-chr12:48731797..48736045,4	MCF-7	breast:
5	chr12:48723401..48726015-chr12:48731031..48733987,2	K562	blood:
6	chr12:48732421..48734160-chr12:48734497..48737400,2	MCF-7	breast:
7	chr12:48727537..48730148-chr12:48731988..48733815,2	MCF-7	breast:
8	chr12:48731903..48736039-chr12:48740955..48745883,6	MCF-7	breast:
9	chr12:48718327..48723671-chr12:48729178..48735713,9	MCF-7	breast:
10	chr12:48704261..48706305-chr12:48731702..48733217,2	K562	blood:
11	chr12:48727374..48736715-chr12:48738720..48747602,13	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258273	TF binding region
ENSG00000226413	Chromatin interaction
ENSG00000187166	Chromatin interaction
ENSG00000257735	Chromatin interaction
ENSG00000258273	Chromatin interaction
ENSG00000167528	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1061986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875753	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs1107654	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168428	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs11168437	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap]
rs11168468	0.83[EUR][1000 genomes]
rs11168474	0.82[EUR][1000 genomes]
rs11168484	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12828309	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12829841	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1387259	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1387260	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1489108	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1542707	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1552550	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1601985	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2054905	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2409003	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2409004	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2450994	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2450996	0.84[EUR][1000 genomes]
rs2468943	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs2468949	0.82[EUR][1000 genomes]
rs2634670	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634681	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2634682	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2634684	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634686	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2634688	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2634689	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2634691	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634692	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634693	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634694	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732441	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2732445	0.81[AMR][1000 genomes]
rs2732448	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2732453	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2732454	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2732457	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732461	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2732462	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2732479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732480	0.95[GIH][hapmap];0.85[MEX][hapmap]
rs2732481	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732484	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732486	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732488	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956703	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2956710	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34286639	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6580662	0.83[EUR][1000 genomes]
rs7297824	0.92[CEU][hapmap]
rs7301003	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs7307566	0.81[EUR][1000 genomes]
rs7315820	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs7486941	1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap]
rs7487682	1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap]
rs7959684	1.00[CHD][hapmap]
rs7960122	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7966829	0.82[EUR][1000 genomes]
rs8716	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs923397	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv437752	chr12:48721832-48741219	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv438208	chr12:48724778-48734609	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
11	nsv1044444	chr12:48725007-48737570	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
12	esv1008169	chr12:48725141-48732917	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
13	nsv1045159	chr12:48730024-48748940	Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2732466	H1FNT	cis	Muscle Skeletal	GTEx
rs2732466	ZNF641	cis	cerebellum	SCAN
rs2732466	FKBP11	cis	cerebellum	SCAN
rs2732466	H1FNT	cis	Artery Tibial	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48723800-48736600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:48724200-48734400	Weak transcription	Thymus	Thymus
3	chr12:48724400-48736000	Weak transcription	Fetal Stomach	stomach
4	chr12:48725200-48734600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr12:48725200-48735800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr12:48725200-48736800	Weak transcription	Hela-S3	cervix
7	chr12:48728000-48736000	Weak transcription	HSMMtube	muscle
8	chr12:48728600-48734000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr12:48728600-48734800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr12:48728800-48733400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr12:48728800-48734000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:48728800-48736600	Weak transcription	Right Ventricle	heart
13	chr12:48728800-48737000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:48729000-48732800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr12:48729000-48733400	Weak transcription	Adipose Nuclei	Adipose
16	chr12:48729000-48734400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:48729000-48735600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:48729000-48735800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:48729000-48736000	Weak transcription	Spleen	Spleen
20	chr12:48729000-48736400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr12:48729000-48739200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:48729200-48732600	Weak transcription	Primary T cells from cord blood	blood
23	chr12:48729200-48733000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr12:48729200-48736600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:48729200-48736600	Weak transcription	Fetal Intestine Small	intestine
26	chr12:48729200-48736600	Weak transcription	Pancreas	Pancrea
27	chr12:48729200-48743400	Weak transcription	Stomach Mucosa	stomach
28	chr12:48729400-48733600	Weak transcription	Primary B cells from cord blood	blood
29	chr12:48729400-48736000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:48729600-48734200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:48730000-48733400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:48730000-48736000	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:48730200-48736000	Weak transcription	Placenta	Placenta
34	chr12:48730200-48736600	Weak transcription	Ovary	ovary
35	chr12:48730400-48732600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:48730400-48736400	Weak transcription	Lung	lung
37	chr12:48730600-48734000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:48730600-48736800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr12:48730800-48736000	Weak transcription	Brain Angular Gyrus	brain
40	chr12:48731000-48732600	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:48731000-48732600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr12:48731000-48734000	Weak transcription	Fetal Brain Female	brain
43	chr12:48731000-48736000	Weak transcription	Fetal Lung	lung
44	chr12:48731000-48736400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:48731200-48733600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr12:48731200-48738200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:48731200-48743800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr12:48731400-48736200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr12:48731400-48736800	Weak transcription	Psoas Muscle	Psoas
50	chr12:48731600-48733200	Weak transcription	Brain Hippocampus Middle	brain

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