Variant report

Variant	rs10880807
Chromosome Location	chr12:45912862-45912863
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	chr12:45911413..45913925-chr12:46121246..46124442,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCAF11-1	chr12:45912837-45912936	ENSG00000257657.1
2	lnc-SCAF11-1	chr12:45912837-45912936	ENSG00000257657.2

Variant related genes	Relation type
ENSG00000189079	Chromatin interaction
ENSG00000273015	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10736027	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10785575	0.82[ASN][1000 genomes]
rs10785576	0.92[ASN][1000 genomes]
rs10785578	0.97[ASN][1000 genomes]
rs10880791	0.82[ASN][1000 genomes]
rs10880794	0.90[ASN][1000 genomes]
rs10880798	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880799	0.81[EUR][1000 genomes]
rs10880800	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10880803	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880804	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880805	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10880806	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183067	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183068	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183069	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183070	0.81[EUR][1000 genomes]
rs11183071	0.81[EUR][1000 genomes]
rs11183072	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11183077	0.93[ASN][1000 genomes]
rs11183078	0.93[ASN][1000 genomes]
rs11183079	0.93[ASN][1000 genomes]
rs12228136	0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs12297127	0.83[EUR][1000 genomes]
rs12298570	0.93[ASN][1000 genomes]
rs12303053	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12303153	0.81[EUR][1000 genomes]
rs12303449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316574	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12317115	0.93[ASN][1000 genomes]
rs12320604	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12321802	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12830355	0.81[EUR][1000 genomes]
rs12830362	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12832353	0.81[EUR][1000 genomes]
rs17096009	0.84[ASN][1000 genomes]
rs2408255	0.83[ASN][1000 genomes]
rs2408272	0.90[ASN][1000 genomes]
rs2408318	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2408323	0.90[ASN][1000 genomes]
rs2897904	0.81[EUR][1000 genomes]
rs2897905	0.84[ASN][1000 genomes]
rs33971594	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34265125	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34331166	0.81[EUR][1000 genomes]
rs34865395	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35296382	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35449278	0.81[EUR][1000 genomes]
rs4378456	0.81[EUR][1000 genomes]
rs4567534	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4570651	0.90[ASN][1000 genomes]
rs4590938	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768090	0.92[ASN][1000 genomes]
rs4768091	0.91[ASN][1000 genomes]
rs4768623	0.90[ASN][1000 genomes]
rs5001653	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5003954	0.84[ASN][1000 genomes]
rs56217910	0.84[ASN][1000 genomes]
rs7133173	0.87[ASN][1000 genomes]
rs73285289	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7486952	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7968560	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832395	chr12:45841765-46039297	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv508672	chr12:45884730-45931091	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv1791767	chr12:45892993-45912862	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv691	chr12:45896295-45946455	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv511498	chr12:45901586-45912862	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv558760	chr12:45901586-45913177	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv558761	chr12:45901586-45924964	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1792250	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1796155	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv1803091	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1803348	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1807521	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1808857	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv1814107	chr12:45903118-45912862	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv1828597	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv1830594	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv1834808	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv1836843	chr12:45903118-45912862	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv1842350	chr12:45903118-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	esv1842210	chr12:45903118-45940761	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	esv1802574	chr12:45903265-45912862	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv558766	chr12:45903265-45912862	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv558767	chr12:45903265-45913177	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv558776	chr12:45903913-45913177	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45910600-45913800	Enhancers	Fetal Thymus	thymus
2	chr12:45911000-45913000	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr12:45911400-45913000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:45911800-45913000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr12:45911800-45913000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:45911800-45913200	Enhancers	Primary T cells from cord blood	blood
7	chr12:45911800-45913200	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr12:45912000-45913000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr12:45912000-45913000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:45912000-45913200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:45912000-45913200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr12:45912000-45913200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr12:45912200-45913000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr12:45912200-45913000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:45912200-45913000	Enhancers	NHEK	skin
16	chr12:45912400-45913000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:45912400-45913200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:45912600-45913000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr12:45912800-45913000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr12:45912800-45913000	Enhancers	GM12878-XiMat	blood
21	chr12:45912800-45913200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:45912800-45914000	Enhancers	Thymus	Thymus
23	chr12:45912800-45916000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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