Variant report

Variant	rs12593880
Chromosome Location	chr15:58779641-58779642
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	chr15:58758547..58760128-chr15:58777523..58780209,2	MCF-7	breast:
2	chr15:58778802..58780678-chr15:58783257..58786951,3	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10518978	0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11634902	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12591216	0.81[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs12591624	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs12592407	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593736	0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12594222	0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs12595191	0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12900891	0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12902119	0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12903955	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12906459	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs12908427	0.93[ASN][1000 genomes]
rs12910028	0.85[ASN][1000 genomes]
rs12910602	0.89[ASN][1000 genomes]
rs12913605	0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs16940338	0.81[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs17190580	0.90[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs17190587	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2414581	0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28478642	0.85[ASN][1000 genomes]
rs2899630	0.98[ASN][1000 genomes]
rs34053638	0.83[ASN][1000 genomes]
rs34297592	0.83[ASN][1000 genomes]
rs34570549	0.83[ASN][1000 genomes]
rs34577128	0.81[ASN][1000 genomes]
rs34744603	0.83[ASN][1000 genomes]
rs35633916	0.83[ASN][1000 genomes]
rs35732576	0.83[ASN][1000 genomes]
rs35771822	0.98[ASN][1000 genomes]
rs35795657	0.98[ASN][1000 genomes]
rs4775053	0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs6494009	0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs6494010	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs6494011	0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs71478668	0.90[ASN][1000 genomes]
rs71478670	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71478671	0.91[ASN][1000 genomes]
rs71478672	0.89[ASN][1000 genomes]
rs7162384	0.89[ASN][1000 genomes]
rs7162603	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7169744	0.81[ASN][1000 genomes]
rs7172556	0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7174539	0.83[ASN][1000 genomes]
rs8029592	0.98[ASN][1000 genomes]
rs8029837	0.98[ASN][1000 genomes]
rs8041525	0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1047048	chr15:58701400-58784800	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv904268	chr15:58763678-58803225	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12593880	KIAA1370	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58769600-58780000	Weak transcription	Right Atrium	heart
2	chr15:58770400-58779800	Weak transcription	Left Ventricle	heart
3	chr15:58772400-58779800	Weak transcription	Fetal Kidney	kidney
4	chr15:58774600-58780200	Enhancers	HSMMtube	muscle
5	chr15:58775000-58780600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr15:58775600-58780400	Enhancers	Fetal Thymus	thymus
7	chr15:58775600-58780800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr15:58775600-58781000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:58775800-58780000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr15:58776600-58782400	Weak transcription	Right Ventricle	heart
11	chr15:58777200-58780400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:58777200-58780600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:58777400-58780600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr15:58777400-58780600	Enhancers	Placenta	Placenta
15	chr15:58777600-58780400	Enhancers	Primary T cells from cord blood	blood
16	chr15:58777600-58780800	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr15:58777600-58780800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr15:58777600-58780800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr15:58777600-58780800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr15:58778000-58780200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:58778400-58780000	Weak transcription	Brain Substantia Nigra	brain
22	chr15:58778400-58780200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:58778600-58779800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:58778600-58780000	Weak transcription	Spleen	Spleen
25	chr15:58778600-58780200	Enhancers	Thymus	Thymus
26	chr15:58778600-58780600	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr15:58779200-58784000	Weak transcription	Esophagus	oesophagus
28	chr15:58779200-58784000	Weak transcription	Pancreas	Pancrea
29	chr15:58779400-58779800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:58779400-58780200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:58779400-58783400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr15:58779600-58780200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr15:58779600-58780200	Enhancers	Adipose Nuclei	Adipose
34	chr15:58779600-58780400	Enhancers	Skeletal Muscle Female	skeletal muscle

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