Variant report

Variant	rs679873
Chromosome Location	chr18:7750535-7750536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:7749744..7751445-chr18:7751627..7754409,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10163760	1.00[JPT][hapmap]
rs12165086	0.89[ASN][1000 genomes]
rs12326071	1.00[JPT][hapmap]
rs13380901	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13381592	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1530516	0.89[ASN][1000 genomes]
rs1664980	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4121619	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs599006	0.83[EUR][1000 genomes]
rs608028	0.96[GIH][hapmap]
rs613706	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616019	0.81[CEU][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs629562	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506526	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs658864	0.96[GIH][hapmap]
rs664592	0.85[CEU][hapmap];0.88[GIH][hapmap];0.83[EUR][1000 genomes]
rs678492	0.96[GIH][hapmap]
rs679539	0.81[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs7230332	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7231079	0.89[ASN][1000 genomes]
rs7231089	0.89[ASN][1000 genomes]
rs7239716	0.89[ASN][1000 genomes]
rs727037	0.85[CEU][hapmap]
rs73389600	0.89[ASN][1000 genomes]
rs73391565	0.89[ASN][1000 genomes]
rs8085995	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8089054	0.89[ASN][1000 genomes]
rs9954459	1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064597	chr18:7169490-7762738	Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv543636	chr18:7169490-7762738	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv458016	chr18:7488133-7934001	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv576399	chr18:7488133-7934001	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2762810	chr18:7492090-7924728	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking 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	7 gene(s)	inside rSNPs	diseases
11	nsv1064869	chr18:7730116-7760969	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1061538	chr18:7730116-7762149	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1067394	chr18:7730116-7768536	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv2656311	chr18:7732141-7761056	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1057760	chr18:7732188-7760969	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv431970	chr18:7732188-7770950	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv525328	chr18:7732917-7760498	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv576421	chr18:7732917-7761056	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv576422	chr18:7732917-7763363	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv576423	chr18:7732917-7788329	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv576424	chr18:7740473-7761056	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv576425	chr18:7747873-7859757	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs679873	VAPA	cis	cerebellum	SCAN
rs679873	SOHLH1	trans	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7739000-7750600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:7742000-7751400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr18:7745600-7750800	Weak transcription	Aorta	Aorta
4	chr18:7746800-7751400	Enhancers	Right Ventricle	heart
5	chr18:7746800-7752000	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr18:7746800-7753600	Enhancers	HepG2	liver
7	chr18:7747000-7752000	Enhancers	Fetal Heart	heart
8	chr18:7748000-7751000	Enhancers	HUVEC	blood vessel
9	chr18:7748200-7750600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr18:7748200-7750800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr18:7748200-7751400	Enhancers	Fetal Kidney	kidney
12	chr18:7748400-7750800	Enhancers	Fetal Muscle Leg	muscle
13	chr18:7748400-7751800	Enhancers	A549	lung
14	chr18:7748600-7751400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr18:7748600-7752200	Enhancers	Adipose Nuclei	Adipose
16	chr18:7748600-7784000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr18:7749000-7750600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr18:7749000-7750600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr18:7749000-7751000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr18:7749200-7750600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr18:7749200-7751200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:7749200-7754400	Weak transcription	Gastric	stomach
23	chr18:7749200-7757000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr18:7749600-7750800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr18:7749800-7750600	Weak transcription	Pancreas	Pancrea
26	chr18:7749800-7750800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr18:7749800-7750800	Weak transcription	Lung	lung
28	chr18:7749800-7751000	Weak transcription	Ovary	ovary
29	chr18:7749800-7754400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr18:7749800-7754400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr18:7749800-7754400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr18:7749800-7754400	Weak transcription	Small Intestine	intestine
33	chr18:7749800-7754600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr18:7749800-7755000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr18:7750000-7750800	Active TSS	Thymus	Thymus
36	chr18:7750000-7751000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr18:7750000-7752000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr18:7750000-7753600	Weak transcription	Fetal Intestine Small	intestine
39	chr18:7750000-7753800	Weak transcription	Fetal Intestine Large	intestine
40	chr18:7750000-7754200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr18:7750000-7754200	Weak transcription	Osteobl	bone
42	chr18:7750000-7754600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr18:7750000-7760800	Weak transcription	Fetal Stomach	stomach
44	chr18:7750200-7750600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr18:7750200-7751800	Enhancers	Fetal Lung	lung
46	chr18:7750200-7753800	Weak transcription	Colon Smooth Muscle	Colon
47	chr18:7750200-7754400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr18:7750200-7755000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr18:7750400-7751000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr18:7750400-7751200	Flanking Active TSS	Fetal Thymus	thymus

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