Variant report

Variant	rs12580690
Chromosome Location	chr12:66664348-66664349
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:66562059..66564865-chr12:66662952..66665782,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11176101	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176102	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11176103	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11176104	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11176108	1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176111	0.86[AMR][1000 genomes]
rs11176112	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11176113	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176114	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11176119	1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176123	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12300494	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12301281	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306996	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12307002	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12307547	0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12308374	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12310345	0.90[CHB][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12312158	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12314232	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12314623	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12318122	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12320275	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12320290	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12320341	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12321294	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322090	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12579472	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1436848	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17102269	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2082994	0.86[AMR][1000 genomes]
rs57747494	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7132241	0.91[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313493	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs903585	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9325181	1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9971828	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9971830	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9971831	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9971850	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9971905	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899216	chr12:66563835-66716844	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv976747	chr12:66663300-66669568	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66661000-66664800	Enhancers	Primary T cells from cord blood	blood
2	chr12:66661200-66664600	Enhancers	Primary B cells from cord blood	blood
3	chr12:66661200-66666800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:66661600-66665600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:66662000-66664600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:66662000-66664600	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr12:66662400-66664800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr12:66662600-66664600	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr12:66663200-66665800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr12:66663400-66664400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:66663600-66665800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr12:66663600-66666600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:66663600-66666800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:66663600-66667400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:66663800-66664400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:66663800-66664600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr12:66663800-66665800	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr12:66663800-66666800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:66663800-66667000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:66663800-66667400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:66664000-66666600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:66664000-66666800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:66664200-66664600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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