Variant report

Variant	rs72632838
Chromosome Location	chr1:227979665-227979666
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	chr1:227979105..227980734-chr1:228192803..228195420,2	K562	blood:
3	chr1:227977112..227980203-chr1:227982448..227986232,4	MCF-7	breast:
4	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

Variant related genes	Relation type
ENSG00000154342	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13376549	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6679352	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6688900	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6695545	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6697061	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6704268	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72632837	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7555052	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9651013	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][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:40 , 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	chr1:227976800-227981200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:227976800-227981400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:227976800-227981400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:227976800-227981600	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:227976800-227981600	Weak transcription	Right Atrium	heart
7	chr1:227977000-227981000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:227977000-227981200	Weak transcription	HSMM	muscle
9	chr1:227977000-227981400	Weak transcription	Colonic Mucosa	Colon
10	chr1:227977000-227981800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:227977000-227982000	Weak transcription	Right Ventricle	heart
12	chr1:227977000-227982400	Weak transcription	Brain Angular Gyrus	brain
13	chr1:227977000-227985000	Weak transcription	Gastric	stomach
14	chr1:227977200-227980400	Weak transcription	Ovary	ovary
15	chr1:227977200-227981200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:227977200-227982000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:227977400-227980800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:227977400-227980800	Weak transcription	NH-A	brain
19	chr1:227977400-227980800	Weak transcription	NHLF	lung
20	chr1:227977400-227981200	Weak transcription	HSMMtube	muscle
21	chr1:227977400-227982000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:227977400-227982200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:227977400-227982400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:227977600-227980400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:227977600-227980800	Weak transcription	NHDF-Ad	bronchial
26	chr1:227977600-227981600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:227977600-227982000	Weak transcription	HMEC	breast
28	chr1:227977800-227980000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:227977800-227980000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:227977800-227980800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:227978000-227980000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:227978000-227980000	Enhancers	Fetal Stomach	stomach
33	chr1:227978000-227980200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:227978000-227980400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:227978000-227981200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:227979000-227980000	Enhancers	Fetal Kidney	kidney
37	chr1:227979400-227979800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:227979400-227980400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:227979400-227981400	Weak transcription	Esophagus	oesophagus
40	chr1:227979600-227981000	Enhancers	Fetal Lung	lung

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