Variant report

Variant	rs1180012
Chromosome Location	chr12:121530448-121530449
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	chr12:121528483..121531655-chr12:121531657..121534218,3	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10849844	0.85[CHB][hapmap]
rs11065434	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11065442	0.96[ASN][1000 genomes]
rs11065450	0.91[MEX][hapmap]
rs1180001	0.81[EUR][1000 genomes]
rs1180002	0.81[EUR][1000 genomes]
rs1180003	0.81[EUR][1000 genomes]
rs1180004	0.81[EUR][1000 genomes]
rs1180006	0.81[EUR][1000 genomes]
rs1180011	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1180015	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1182936	0.81[EUR][1000 genomes]
rs1183296	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1185268	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1185890	0.81[EUR][1000 genomes]
rs1186228	0.80[EUR][1000 genomes]
rs169631	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs169632	0.91[ASN][1000 genomes]
rs169633	0.88[ASN][1000 genomes]
rs1794892	0.81[EUR][1000 genomes]
rs1794895	0.81[EUR][1000 genomes]
rs1794896	0.80[EUR][1000 genomes]
rs1794897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796412	0.97[TSI][hapmap]
rs1796421	0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs1796422	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1796423	0.81[EUR][1000 genomes]
rs183283	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs189989	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs208277	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs208280	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs208284	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs208287	0.91[ASN][1000 genomes]
rs208290	0.85[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.90[ASN][1000 genomes]
rs208293	0.95[CHB][hapmap];0.81[JPT][hapmap];0.94[TSI][hapmap]
rs208294	0.90[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs2263270	0.81[EUR][1000 genomes]
rs2263271	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2393799	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516210	0.81[EUR][1000 genomes]
rs2686352	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708091	0.80[EUR][1000 genomes]
rs489793	0.86[AFR][1000 genomes]
rs500930	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs501167	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs570984	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs575572	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs582315	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs591874	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636719	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs656612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs665794	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs671684	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs676262	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs685019	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7309886	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9971689	0.81[EUR][1000 genomes]
rs9971861	0.81[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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1039216	chr12:121421701-121538491	Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv430537	chr12:121487632-121579955	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
12	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1180012	ORAI1	cis	cerebellum	SCAN
rs1180012	PITPNM2	cis	parietal	SCAN
rs1180012	P2RX7	cis	lymphoblastoid	seeQTL
rs1180012	DENR	cis	parietal	SCAN
rs1180012	P2RX4	cis	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121526000-121533400	Weak transcription	Right Ventricle	heart
2	chr12:121527400-121533200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:121528400-121533000	Weak transcription	Adipose Nuclei	Adipose
4	chr12:121528400-121533200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr12:121528600-121531800	Enhancers	Fetal Thymus	thymus
6	chr12:121528600-121533400	Weak transcription	Right Atrium	heart
7	chr12:121529000-121533200	Weak transcription	Left Ventricle	heart
8	chr12:121529200-121531400	Weak transcription	Spleen	Spleen
9	chr12:121529200-121533400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:121529400-121530600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr12:121529400-121531800	Enhancers	Primary hematopoietic stem cells	blood
12	chr12:121529600-121532600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr12:121529600-121533400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:121529600-121533400	Weak transcription	Fetal Heart	heart
15	chr12:121529800-121530600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:121529800-121533400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr12:121529800-121533400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:121530000-121531200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr12:121530200-121530600	Enhancers	GM12878-XiMat	blood
20	chr12:121530200-121530800	Enhancers	Primary B cells from peripheral blood	blood
21	chr12:121530200-121530800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:121530200-121531000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr12:121530200-121531000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:121530200-121531000	Flanking Active TSS	Dnd41	blood
25	chr12:121530400-121530600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:121530400-121530600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr12:121530400-121530600	Enhancers	Primary B cells from cord blood	blood
28	chr12:121530400-121530600	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr12:121530400-121530800	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr12:121530400-121530800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr12:121530400-121530800	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr12:121530400-121530800	Flanking Active TSS	Thymus	Thymus
33	chr12:121530400-121531000	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr12:121530400-121531000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr12:121530400-121531000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:121530400-121531000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:121530400-121531000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr12:121530400-121531000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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