Variant report

Variant	rs5029904
Chromosome Location	chr15:79152422-79152423
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:79147722..79157046-chr15:79163022..79167664,11	K562	blood:
2	chr15:79152332..79153154-chr15:79202006..79202806,3	MCF-7	breast:
3	chr15:79151201..79154383-chr15:79164665..79166709,3	MCF-7	breast:
4	chr15:79149764..79156555-chr15:79163462..79168215,14	K562	blood:
5	chr15:79149806..79152518-chr15:79156758..79158450,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185787	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11072812	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11632020	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11637783	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11857877	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12232282	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12903249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911870	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16970187	0.90[JPT][hapmap]
rs16970254	0.90[JPT][hapmap]
rs28580532	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34184420	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4132786	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4344704	0.93[EUR][1000 genomes]
rs4420501	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4421942	1.00[JPT][hapmap]
rs4438276	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4439728	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4567668	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5849	0.90[JPT][hapmap]
rs7168915	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7173743	0.80[CEU][hapmap];0.93[EUR][1000 genomes]
rs8034274	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8037171	0.94[AMR][1000 genomes];0.92[EUR][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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904432	chr15:79066932-79175813	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79151600-79153200	Active TSS	A549	lung
2	chr15:79151600-79153200	Active TSS	Hela-S3	cervix
3	chr15:79151800-79152800	Active TSS	HSMMtube	muscle
4	chr15:79151800-79153200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:79151800-79153200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:79152000-79152600	Flanking Active TSS	HUVEC	blood vessel
7	chr15:79152000-79152800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:79152000-79152800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:79152000-79152800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:79152000-79152800	Active TSS	HSMM	muscle
11	chr15:79152000-79152800	Active TSS	NH-A	brain
12	chr15:79152000-79153000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:79152000-79153000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:79152000-79153200	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr15:79152000-79153200	Active TSS	H1 Cell Line	embryonic stem cell
16	chr15:79152000-79153200	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr15:79152000-79153200	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr15:79152000-79153200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr15:79152000-79153200	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr15:79152000-79153200	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr15:79152000-79153200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:79152000-79153200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:79152000-79153200	Active TSS	K562	blood
24	chr15:79152000-79153400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:79152200-79152600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:79152200-79152600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:79152200-79152600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:79152200-79152600	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr15:79152200-79152600	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr15:79152200-79152600	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr15:79152200-79152600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr15:79152200-79152600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr15:79152200-79152600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr15:79152200-79152600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr15:79152200-79152600	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr15:79152200-79152600	Flanking Active TSS	Liver	Liver
37	chr15:79152200-79152600	Active TSS	Brain Cingulate Gyrus	brain
38	chr15:79152200-79152600	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr15:79152200-79152600	Active TSS	Stomach Mucosa	stomach
40	chr15:79152200-79152600	Flanking Active TSS	GM12878-XiMat	blood
41	chr15:79152200-79152600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr15:79152200-79152800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr15:79152200-79152800	Active TSS	H9 Cell Line	embryonic stem cell
44	chr15:79152200-79152800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:79152200-79152800	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr15:79152200-79152800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:79152200-79152800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:79152200-79152800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:79152200-79152800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:79152200-79152800	Flanking Active TSS	Primary B cells from cord blood	blood

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