Variant report

Variant	rs7542172
Chromosome Location	chr1:46990681-46990682
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46985914..46991197-chr1:46993744..46997835,5	K562	blood:
2	chr1:46979114..46981984-chr1:46990553..46993126,2	K562	blood:
3	chr1:46972661..46974306-chr1:46990431..46992599,2	K562	blood:
4	chr1:46986798..46990832-chr1:46991693..46995331,8	K562	blood:
5	chr1:46950640..46959255-chr1:46986389..46991936,15	K562	blood:
6	chr1:46911310..46914050-chr1:46990566..46993135,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197587	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12120456	0.93[ASN][1000 genomes]
rs12132747	0.81[ASN][1000 genomes]
rs12409747	0.82[CHB][hapmap]
rs2209172	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs3795315	0.84[CHB][hapmap]
rs4660353	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs56393814	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers 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 target site	17 gene(s)	inside rSNPs	diseases
8	nsv998422	chr1:46969626-47023671	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv534953	chr1:46969626-47023671	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1010578	chr1:46977818-47010579	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Blood metabolite levels	24816252	GWAS catalog

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46986600-46991200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:46987800-46991000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr1:46987800-46993800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:46988400-46992400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:46988400-46992600	Weak transcription	Spleen	Spleen
6	chr1:46988800-46991000	Weak transcription	NH-A	brain
7	chr1:46988800-46998600	Weak transcription	Right Ventricle	heart
8	chr1:46989000-46993200	Weak transcription	Pancreas	Pancrea
9	chr1:46989000-46999000	Weak transcription	Gastric	stomach
10	chr1:46989200-46998600	Weak transcription	Right Atrium	heart
11	chr1:46989400-46990800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:46989400-46992600	Weak transcription	A549	lung
13	chr1:46989600-46991000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:46989800-46990800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
15	chr1:46989800-46994200	Enhancers	K562	blood
16	chr1:46990000-46993800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:46990200-46992600	Weak transcription	Hela-S3	cervix
18	chr1:46990200-46994000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:46990200-46994400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
20	chr1:46990400-46990800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
21	chr1:46990400-46992000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:46990400-46992600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
23	chr1:46990400-46993000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:46990600-46991600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
25	chr1:46990600-46992400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
26	chr1:46990600-46994400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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