Variant report

Variant	rs73930142
Chromosome Location	chr2:38878200-38878201
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:38876173..38878521-chr2:38919650..38921533,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17023025	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17023028	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2163556	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57241175	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57481292	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58917023	0.87[AFR][1000 genomes]
rs59962102	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61420714	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760524	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73930139	0.89[AFR][1000 genomes]
rs7560608	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs891707	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv581485	chr2:38839323-38893660	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv2762495	chr2:38861095-38886391	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3457549	chr2:38871768-38882574	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3457553	chr2:38871805-38882546	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv3457551	chr2:38871805-38882561	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv3457550	chr2:38871849-38882546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	esv14023	chr2:38871950-38882521	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	esv2421758	chr2:38873799-38881106	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	esv2760617	chr2:38873799-38886391	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv516043	chr2:38874177-38881106	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv817740	chr2:38874177-38881106	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38870800-38881600	Weak transcription	Spleen	Spleen
2	chr2:38871200-38880800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:38873200-38879600	Enhancers	K562	blood
4	chr2:38873400-38878400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:38874600-38880800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:38875600-38880600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:38875800-38879200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr2:38875800-38879200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr2:38875800-38879400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:38875800-38879600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:38875800-38879600	Weak transcription	Hela-S3	cervix
12	chr2:38875800-38880600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:38875800-38880800	Weak transcription	HMEC	breast
14	chr2:38876000-38878400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:38876000-38878600	Bivalent Enhancer	HepG2	liver
16	chr2:38876000-38879000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:38876000-38879200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:38876000-38879400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:38876000-38879400	Weak transcription	Fetal Thymus	thymus
20	chr2:38876000-38882000	Weak transcription	Thymus	Thymus
21	chr2:38876200-38879000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:38876200-38879400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr2:38876400-38879600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:38876600-38879000	Weak transcription	Placenta	Placenta
25	chr2:38876600-38880400	Weak transcription	Dnd41	blood
26	chr2:38877000-38878400	Enhancers	Stomach Mucosa	stomach
27	chr2:38877200-38878800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:38877200-38882000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:38877200-38882200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:38877600-38879400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr2:38877800-38878200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr2:38877800-38878200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:38877800-38879400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:38877800-38880000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:38878000-38878200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:38878200-38879600	Enhancers	GM12878-XiMat	blood
37	chr2:38878200-38880800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:38878200-38888400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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