Variant report

Variant	rs4477671
Chromosome Location	chr15:34329673-34329674
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:34320977..34323643-chr15:34328767..34331333,2	MCF-7	breast:
2	chr15:34299066..34301596-chr15:34326883..34329699,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11072868	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635479	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898898	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903907	0.96[EUR][1000 genomes]
rs12913747	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339352	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684940	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34474029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34773983	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35531038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35804445	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779652	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4780203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536345	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602302	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618868	0.87[EUR][1000 genomes]
rs62014670	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62014671	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs632591	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495442	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495443	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66530874	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67739072	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71462883	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71464844	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7162140	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168640	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7169003	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173183	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175823	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178075	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178446	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72718678	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72718682	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030094	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033781	0.84[AMR][1000 genomes];0.81[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	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv903985	chr15:34279319-34370487	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4477671	AVEN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34309400-34330000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:34309600-34330000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr15:34320200-34329800	Weak transcription	Hela-S3	cervix
4	chr15:34323000-34330000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:34324800-34329800	Weak transcription	Brain Angular Gyrus	brain
6	chr15:34326600-34330200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:34327000-34330000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:34327200-34329800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:34327200-34330000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:34327400-34330000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:34327400-34330000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:34327400-34330000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr15:34327600-34329800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:34327600-34330000	Weak transcription	Fetal Heart	heart
15	chr15:34327600-34330000	Weak transcription	Fetal Kidney	kidney
16	chr15:34327800-34330000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:34327800-34330000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr15:34327800-34330000	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:34327800-34330000	Weak transcription	Fetal Brain Male	brain
20	chr15:34328000-34330000	Weak transcription	Fetal Lung	lung
21	chr15:34328200-34329800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:34328200-34329800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:34328200-34330000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:34328200-34330000	Weak transcription	Fetal Stomach	stomach
25	chr15:34328400-34330000	Weak transcription	NHDF-Ad	bronchial
26	chr15:34328400-34330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:34328600-34330000	Enhancers	NHLF	lung
28	chr15:34329000-34330000	Weak transcription	Brain Anterior Caudate	brain
29	chr15:34329200-34330000	Weak transcription	HSMM	muscle
30	chr15:34329400-34329800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:34329400-34329800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr15:34329400-34329800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:34329400-34329800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:34329400-34329800	Enhancers	Dnd41	blood
35	chr15:34329400-34329800	Enhancers	HMEC	breast
36	chr15:34329400-34330000	Enhancers	Liver	Liver
37	chr15:34329400-34330000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr15:34329400-34330000	Enhancers	Osteobl	bone
39	chr15:34329400-34331600	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr15:34329600-34329800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:34329600-34329800	Enhancers	A549	lung
42	chr15:34329600-34330000	Enhancers	Primary B cells from cord blood	blood
43	chr15:34329600-34331600	Active TSS	GM12878-XiMat	blood

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