Variant report

Variant	rs11723554
Chromosome Location	chr4:15673337-15673338
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:15653293..15659319-chr4:15668815..15673574,11	MCF-7	breast:
2	chr4:15655677..15658651-chr4:15671837..15675305,4	MCF-7	breast:
3	chr4:15664653..15666973-chr4:15669930..15673591,3	MCF-7	breast:
4	chr4:15673240..15674969-chr4:15677739..15681015,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10001565	0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10017222	1.00[CHB][hapmap]
rs10516289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729955	1.00[CHB][hapmap]
rs11730336	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12643475	0.90[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12646913	0.90[CEU][hapmap];1.00[CHD][hapmap]
rs12650632	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17405811	1.00[CHB][hapmap]
rs17406128	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476642	1.00[CHB][hapmap]
rs1786	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs28532698	0.86[ASN][1000 genomes]
rs34910084	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3756247	1.00[CHB][hapmap]
rs4301111	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs4301112	0.92[ASN][1000 genomes]
rs4396986	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs4423870	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs4549375	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs56089642	0.85[ASN][1000 genomes]
rs62290586	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62290588	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62290591	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62290593	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62290595	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414764	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs6815254	1.00[CHB][hapmap];0.85[YRI][hapmap]
rs6815296	1.00[CHB][hapmap]
rs6824422	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs6825051	0.80[YRI][hapmap]
rs6826058	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs6827406	1.00[CHB][hapmap]
rs6839654	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs6848779	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs73239201	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7434484	1.00[CHB][hapmap]
rs7667512	0.90[CEU][hapmap]
rs7672311	0.90[CEU][hapmap];1.00[CHD][hapmap]
rs9942212	0.84[ASN][1000 genomes]
rs9994518	0.85[CHB][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv3361772	chr4:15666732-15684418	Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11723554	BST1	cis	multi-tissue	Pritchard
rs11723554	LOC285550	cis	multi-tissue	Pritchard

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15657600-15681400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:15658000-15673800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:15658000-15675200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:15658000-15679000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:15658000-15681400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:15658200-15679200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:15658200-15679200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:15658200-15682200	Weak transcription	Fetal Stomach	stomach
9	chr4:15658600-15679000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr4:15659800-15678600	Weak transcription	K562	blood
11	chr4:15660400-15679200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:15661600-15678600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:15662400-15678800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:15664800-15681800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:15667400-15675200	Weak transcription	Fetal Intestine Large	intestine
16	chr4:15667800-15673800	Weak transcription	Fetal Intestine Small	intestine
17	chr4:15668000-15676400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:15668200-15678600	Weak transcription	NHLF	lung
19	chr4:15668400-15679000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:15668400-15682800	Weak transcription	Fetal Brain Male	brain
21	chr4:15668600-15677000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr4:15668600-15678800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:15668600-15679000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:15668600-15681400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:15668800-15678600	Weak transcription	Hela-S3	cervix
26	chr4:15669000-15677600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:15669000-15679000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:15669400-15673800	Weak transcription	Fetal Thymus	thymus
29	chr4:15669400-15678600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:15669400-15678800	Weak transcription	Osteobl	bone
31	chr4:15669600-15679000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr4:15669600-15679000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:15669600-15679000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:15669600-15681400	Weak transcription	Thymus	Thymus
35	chr4:15669800-15676600	Weak transcription	GM12878-XiMat	blood
36	chr4:15670800-15673400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:15670800-15673400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:15671000-15673400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:15671000-15678800	Weak transcription	NHDF-Ad	bronchial
40	chr4:15671000-15679000	Weak transcription	HUVEC	blood vessel
41	chr4:15671000-15679200	Weak transcription	Fetal Heart	heart
42	chr4:15671000-15679400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr4:15671000-15681600	Weak transcription	Fetal Lung	lung
44	chr4:15671400-15679000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:15672000-15679000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:15672200-15679000	Weak transcription	HepG2	liver
47	chr4:15672600-15673800	Enhancers	Placenta	Placenta
48	chr4:15672600-15675400	Weak transcription	Primary B cells from cord blood	blood
49	chr4:15672800-15674000	Strong transcription	NH-A	brain
50	chr4:15672800-15674400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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