Variant report

Variant	rs73098933
Chromosome Location	chr1:227977844-227977845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227963946..227966853-chr1:227977108..227980456,3	MCF-7	breast:
2	chr1:227977112..227980203-chr1:227982448..227986232,4	MCF-7	breast:
3	chr1:227976724..227980772-chr1:227980865..227984605,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNAP47-1	chr1:227975807-227979880	NONHSAT009949

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs16847987	1.00[AMR][1000 genomes]
rs2101862	1.00[AMR][1000 genomes]
rs2313220	1.00[AMR][1000 genomes]
rs58322371	1.00[AMR][1000 genomes]
rs59404931	1.00[AMR][1000 genomes]
rs59772630	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61283390	1.00[AMR][1000 genomes]
rs6675470	1.00[AMR][1000 genomes]
rs73092610	1.00[AMR][1000 genomes]
rs73092646	1.00[AMR][1000 genomes]
rs73092653	1.00[AMR][1000 genomes]
rs73092661	1.00[AMR][1000 genomes]
rs73092665	1.00[AMR][1000 genomes]
rs73093304	1.00[AMR][1000 genomes]
rs73093319	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73093328	1.00[AMR][1000 genomes]
rs73093344	1.00[AMR][1000 genomes]
rs73093354	1.00[AMR][1000 genomes]
rs73094528	1.00[AMR][1000 genomes]
rs73094536	1.00[AMR][1000 genomes]
rs73094538	1.00[AMR][1000 genomes]
rs73094556	1.00[AMR][1000 genomes]
rs73094558	1.00[AMR][1000 genomes]
rs73094561	1.00[AMR][1000 genomes]
rs73094571	1.00[AMR][1000 genomes]
rs73098926	1.00[AMR][1000 genomes]
rs73099300	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73099302	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73101625	1.00[AMR][1000 genomes]
rs73101653	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7526436	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7555208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9726139	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
11	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227976600-227980600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:227976800-227978000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr1:227976800-227981200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:227976800-227981400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:227976800-227981400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:227976800-227981600	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:227976800-227981600	Weak transcription	Right Atrium	heart
8	chr1:227977000-227978000	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr1:227977000-227978000	Bivalent Enhancer	Fetal Stomach	stomach
10	chr1:227977000-227979000	Weak transcription	Fetal Lung	lung
11	chr1:227977000-227981000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:227977000-227981200	Weak transcription	HSMM	muscle
13	chr1:227977000-227981400	Weak transcription	Colonic Mucosa	Colon
14	chr1:227977000-227981800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:227977000-227982000	Weak transcription	Right Ventricle	heart
16	chr1:227977000-227982400	Weak transcription	Brain Angular Gyrus	brain
17	chr1:227977000-227985000	Weak transcription	Gastric	stomach
18	chr1:227977200-227978000	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr1:227977200-227980400	Weak transcription	Ovary	ovary
20	chr1:227977200-227981200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:227977200-227982000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:227977400-227980800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:227977400-227980800	Weak transcription	NH-A	brain
24	chr1:227977400-227980800	Weak transcription	NHLF	lung
25	chr1:227977400-227981200	Weak transcription	HSMMtube	muscle
26	chr1:227977400-227982000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:227977400-227982200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:227977400-227982400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:227977600-227978000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:227977600-227978400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr1:227977600-227979400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:227977600-227980400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr1:227977600-227980800	Weak transcription	NHDF-Ad	bronchial
34	chr1:227977600-227981600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:227977600-227982000	Weak transcription	HMEC	breast
36	chr1:227977800-227978000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:227977800-227978000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:227977800-227978000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:227977800-227979000	Weak transcription	Esophagus	oesophagus
40	chr1:227977800-227980000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:227977800-227980000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:227977800-227980800	Weak transcription	Placenta Amnion	Placenta Amnion

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