Variant report

Variant	rs12904469
Chromosome Location	chr15:50584368-50584369
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	chr15:50569600..50571427-chr15:50584025..50585795,2	K562	blood:
2	chr15:50581897..50584737-chr15:50644963..50647895,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244879	Chromatin interaction
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11630063	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11631197	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11637975	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12904711	0.91[EUR][1000 genomes]
rs12906304	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12908591	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12909337	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12910368	0.86[AMR][1000 genomes]
rs12912679	0.81[ASN][1000 genomes]
rs12923	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs28451583	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs28453939	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28531946	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs28534445	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28690939	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28719982	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34143694	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34312018	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34405772	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs35013067	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35033384	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs35354250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35446819	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35453213	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4774559	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4775872	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4775873	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs526952	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59514998	0.84[AMR][1000 genomes]
rs7164375	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7164377	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7164798	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7175150	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7183422	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73399285	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8024514	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8030952	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8034597	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs8042053	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8043475	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50567600-50593000	Weak transcription	NHDF-Ad	bronchial
2	chr15:50568000-50593400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:50568200-50592000	Weak transcription	NHLF	lung
4	chr15:50568800-50591800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:50568800-50592200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr15:50568800-50599200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:50569200-50591800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:50569200-50592200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:50569800-50585400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:50570000-50591800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:50570200-50591800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:50570400-50606600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:50570800-50591800	Weak transcription	HSMMtube	muscle
14	chr15:50570800-50600600	Weak transcription	Spleen	Spleen
15	chr15:50571000-50592000	Weak transcription	Right Ventricle	heart
16	chr15:50571200-50593000	Weak transcription	Fetal Kidney	kidney
17	chr15:50572000-50589600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:50572800-50593200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:50573000-50592000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:50573400-50590200	Weak transcription	HMEC	breast
21	chr15:50574400-50602000	Weak transcription	Small Intestine	intestine
22	chr15:50574800-50592000	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:50575000-50588200	Weak transcription	Hela-S3	cervix
24	chr15:50575000-50589800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:50575200-50601000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:50576000-50585200	Strong transcription	Liver	Liver
27	chr15:50576000-50585800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:50576000-50590200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr15:50576000-50592000	Weak transcription	Brain Anterior Caudate	brain
30	chr15:50576200-50585000	Strong transcription	Fetal Thymus	thymus
31	chr15:50576200-50585600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:50576600-50599000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr15:50578200-50592000	Weak transcription	NH-A	brain
34	chr15:50578200-50600400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr15:50578400-50597800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:50578600-50591200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr15:50578600-50592000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr15:50578600-50592600	Weak transcription	Brain Angular Gyrus	brain
39	chr15:50579200-50590000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr15:50579200-50592000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:50579200-50593400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr15:50579400-50585200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr15:50579400-50585400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:50579600-50584400	Strong transcription	Fetal Intestine Small	intestine
45	chr15:50579600-50585200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr15:50580400-50589800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr15:50580400-50591400	Weak transcription	Osteobl	bone
48	chr15:50580400-50599200	Weak transcription	Fetal Brain Male	brain
49	chr15:50580400-50605000	Weak transcription	Fetal Heart	heart
50	chr15:50580600-50596000	Weak transcription	Fetal Brain Female	brain

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