Variant report

Variant	rs12904784
Chromosome Location	chr15:57202918-57202919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57200840..57203668-chr15:57205657..57207213,2	K562	blood:
2	chr15:57178804..57180987-chr15:57202358..57204710,2	MCF-7	breast:
3	chr15:57202329..57204698-chr15:57207841..57211476,5	K562	blood:
4	chr15:57178897..57180716-chr15:57201391..57203977,3	K562	blood:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11630195	0.83[ASN][1000 genomes]
rs11631228	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11631732	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11632592	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11858471	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12899187	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12900986	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12901780	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12906873	0.83[ASN][1000 genomes]
rs12906936	0.83[ASN][1000 genomes]
rs12908670	0.86[ASN][1000 genomes]
rs12914625	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12916237	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12916958	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17819700	0.83[ASN][1000 genomes]
rs2053472	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2111891	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2116065	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2116066	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs213164	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2165461	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2414490	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2583108	0.89[ASN][1000 genomes]
rs2585082	0.86[ASN][1000 genomes]
rs34262415	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35646942	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3803454	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3803455	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4399497	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774898	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774899	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774902	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62022986	0.81[AMR][1000 genomes]
rs62025331	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs715338	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv833020	chr15:57055947-57216068	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv457162	chr15:57083006-57225766	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv569577	chr15:57083006-57225766	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57180200-57208000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr15:57181600-57204000	Weak transcription	Thymus	Thymus
3	chr15:57182000-57209200	Weak transcription	Fetal Stomach	stomach
4	chr15:57182600-57204200	Weak transcription	Fetal Thymus	thymus
5	chr15:57191800-57208000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:57194400-57208600	Weak transcription	Left Ventricle	heart
7	chr15:57196000-57205800	Weak transcription	HSMMtube	muscle
8	chr15:57196200-57207800	Weak transcription	Fetal Brain Female	brain
9	chr15:57197600-57207200	Weak transcription	Fetal Muscle Leg	muscle
10	chr15:57199000-57209000	Weak transcription	Brain Germinal Matrix	brain
11	chr15:57199200-57209000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:57199400-57209200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:57199600-57203000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:57199600-57203000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:57199600-57209000	Weak transcription	Brain Hippocampus Middle	brain
16	chr15:57199600-57209200	Weak transcription	Psoas Muscle	Psoas
17	chr15:57200000-57208000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:57200000-57209000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr15:57200000-57209000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr15:57200200-57205400	Weak transcription	Dnd41	blood
21	chr15:57200200-57205800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:57200200-57209000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:57200200-57209000	Weak transcription	Liver	Liver
24	chr15:57200200-57209200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr15:57200200-57209200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr15:57200200-57209200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:57200400-57207600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:57200400-57209000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr15:57200400-57209000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr15:57200400-57209200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:57201800-57208000	Weak transcription	Fetal Lung	lung
32	chr15:57202600-57209600	Weak transcription	NH-A	brain
33	chr15:57202800-57203000	Enhancers	Brain Angular Gyrus	brain
34	chr15:57202800-57203200	Enhancers	Brain Inferior Temporal Lobe	brain

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