Variant report

Variant	rs901964
Chromosome Location	chr12:48676038-48676039
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48591795..48593507-chr12:48675174..48677324,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269514	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10492080	0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs1074174	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10783231	0.95[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs10783232	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap]
rs10783237	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10783239	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11168451	0.95[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11168455	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap]
rs11609399	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12822085	0.95[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs1387256	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1476608	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs1489111	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552551	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17122651	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs1906718	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1968071	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs2013956	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2054902	0.86[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2130095	0.89[ASN][1000 genomes]
rs2130096	0.80[ASN][1000 genomes]
rs2258342	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2468947	0.83[ASN][1000 genomes]
rs2634679	0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2634685	0.83[CEU][hapmap]
rs2634699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2634701	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732440	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2732443	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732446	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2732451	0.89[ASN][1000 genomes]
rs2732455	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2732458	0.82[GIH][hapmap];0.87[MEX][hapmap]
rs2732464	0.80[ASN][1000 genomes]
rs2732474	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2732475	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2732476	0.96[ASN][1000 genomes]
rs2732477	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2732478	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2732487	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2932091	0.83[CEU][hapmap]
rs2932106	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2932107	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2956704	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3989427	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4075913	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4141065	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4760620	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4760623	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4760685	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4760692	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs4760698	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap]
rs60908321	0.84[ASN][1000 genomes]
rs6580656	0.85[CHB][hapmap]
rs6580660	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7134201	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7134565	0.89[ASN][1000 genomes]
rs726354	0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs7294641	0.84[ASN][1000 genomes]
rs7296913	0.85[JPT][hapmap]
rs7304709	0.93[ASN][1000 genomes]
rs7312326	0.81[JPT][hapmap]
rs7315258	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7485057	0.86[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap]
rs757556	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7953726	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7963934	0.81[JPT][hapmap]
rs7969749	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs879242	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs901962	0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs901963	0.81[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs9645811	0.96[ASN][1000 genomes]
rs987986	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv899062	chr12:48658212-48711867	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv899063	chr12:48664989-48713768	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv899064	chr12:48664989-48721832	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv899065	chr12:48667019-48711867	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv899066	chr12:48667019-48713768	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	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
12	esv34952	chr12:48672333-48703533	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv469369	chr12:48675783-48711867	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv469370	chr12:48675783-48711867	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv469372	chr12:48675783-48711867	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv470290	chr12:48675783-48711867	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv558791	chr12:48675783-48711867	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs901964	PRKAG1	cis	parietal	SCAN
rs901964	ZNF641	cis	multi-tissue	Pritchard
rs901964	ZNF641	cis	Muscle Skeletal	GTEx
rs901964	H1T2	cis	multi-tissue	Pritchard
rs901964	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48672000-48681000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:48673400-48676200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:48674200-48680200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr12:48674600-48681000	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr12:48675400-48676200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:48675400-48676400	Enhancers	Hela-S3	cervix
7	chr12:48675400-48676800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr12:48675600-48676200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:48675600-48676400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:48675800-48676200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr12:48676000-48676200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:48676000-48676200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:48676000-48676400	Bivalent Enhancer	Primary B cells from cord blood	blood

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