Variant report

Variant	rs62007681
Chromosome Location	chr14:103884651-103884652
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:103878753..103883496-chr14:103884428..103888484,4	MCF-7	breast:
2	chr14:103878188..103883188-chr14:103884541..103889590,5	MCF-7	breast:
3	chr14:103883876..103886732-chr14:103888841..103890509,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244691	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10133035	0.81[EUR][1000 genomes]
rs10134580	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1013650	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10139279	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10141120	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10141388	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10141433	0.88[EUR][1000 genomes]
rs10143247	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10145793	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10150072	0.84[EUR][1000 genomes]
rs1028613	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621510	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11622356	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11623869	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624367	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11626483	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11626787	0.80[EUR][1000 genomes]
rs11628213	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11628969	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12879085	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12888077	0.91[EUR][1000 genomes]
rs12889639	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12890750	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12898029	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17617941	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17679475	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1951392	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1961600	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1989565	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2010281	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273699	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2273700	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2273703	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2403180	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28361338	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28369539	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28444993	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28496120	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28583452	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28626081	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34216351	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3742458	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3783394	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3783395	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3783402	0.85[EUR][1000 genomes]
rs3825566	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4900572	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4906321	0.90[EUR][1000 genomes]
rs55723020	0.80[EUR][1000 genomes]
rs55859054	0.83[EUR][1000 genomes]
rs56365443	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62006268	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62007683	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62007684	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62007686	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62007687	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62007718	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62007719	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6575983	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6575984	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7140564	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7145113	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7146506	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7150317	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7152202	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7154246	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7155014	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7156150	0.86[EUR][1000 genomes]
rs7158144	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7158822	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7160208	0.87[EUR][1000 genomes]
rs7160366	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72708854	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72708874	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72708893	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72710714	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8013101	0.88[EUR][1000 genomes]
rs8015918	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8019578	0.84[EUR][1000 genomes]
rs9671911	0.85[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	nsv1049747	chr14:103126148-103955984	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
2	nsv534254	chr14:103470073-104023906	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv9168	chr14:103531729-103913306	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62007681	BAG5	cis	multi-tissue	Pritchard
rs62007681	MARK3	cis	Thyroid	GTEx
rs62007681	BAG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:103862000-103919400	Weak transcription	Colonic Mucosa	Colon
2	chr14:103874600-103900800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr14:103875200-103888200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr14:103875200-103889200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr14:103875200-103893600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr14:103875400-103887400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr14:103875400-103888600	Weak transcription	Gastric	stomach
8	chr14:103875400-103889600	Weak transcription	Colon Smooth Muscle	Colon
9	chr14:103875400-103892200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr14:103875400-103893600	Weak transcription	Brain Germinal Matrix	brain
11	chr14:103875600-103893800	Weak transcription	Fetal Heart	heart
12	chr14:103875600-103894000	Weak transcription	Fetal Brain Male	brain
13	chr14:103875800-103889800	Weak transcription	Lung	lung
14	chr14:103876800-103887800	Weak transcription	Pancreas	Pancrea
15	chr14:103879000-103892800	Weak transcription	Spleen	Spleen
16	chr14:103879000-103895200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr14:103879000-103914200	Weak transcription	Esophagus	oesophagus
18	chr14:103879000-103941400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr14:103879200-103887200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr14:103879600-103889400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr14:103879800-103887400	Weak transcription	HepG2	liver
22	chr14:103880400-103894200	Weak transcription	Liver	Liver
23	chr14:103880400-103904600	Weak transcription	Fetal Kidney	kidney
24	chr14:103881000-103887000	Weak transcription	Thymus	Thymus
25	chr14:103881000-103889200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr14:103881000-103890600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr14:103881000-103900600	Weak transcription	Placenta	Placenta
28	chr14:103882000-103886000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr14:103882000-103887200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr14:103882600-103885000	Enhancers	Adipose Nuclei	Adipose
31	chr14:103882600-103885200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr14:103882600-103886800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr14:103882800-103885000	Enhancers	Brain Cingulate Gyrus	brain
34	chr14:103882800-103885600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr14:103883000-103885000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr14:103883000-103885000	Enhancers	Brain Angular Gyrus	brain
37	chr14:103883000-103885000	Enhancers	Brain Substantia Nigra	brain
38	chr14:103883000-103885000	Enhancers	Left Ventricle	heart
39	chr14:103883000-103885400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr14:103883000-103886200	Enhancers	Brain Hippocampus Middle	brain
41	chr14:103883000-103894400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr14:103883200-103884800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr14:103883200-103885000	Enhancers	Aorta	Aorta
44	chr14:103883200-103885000	Enhancers	HSMMtube	muscle
45	chr14:103883200-103885200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr14:103883200-103885200	Enhancers	Primary hematopoietic stem cells	blood
47	chr14:103883200-103885400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr14:103883200-103885400	Enhancers	Muscle Satellite Cultured Cells	--
49	chr14:103883200-103885400	Enhancers	HSMM	muscle
50	chr14:103883200-103885400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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