Variant report

Variant	rs10799454
Chromosome Location	chr1:228079192-228079193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228078454..228080145-chr1:228100152..228102991,2	MCF-7	breast:
2	chr1:228077305..228079479-chr1:228079746..228085287,6	K562	blood:
3	chr1:228070680..228073922-chr1:228077566..228080384,3	MCF-7	breast:
4	chr1:228077739..228080091-chr1:228081013..228085287,5	K562	blood:
5	chr1:228070687..228073614-chr1:228077834..228079933,2	MCF-7	breast:
6	chr1:228077853..228079489-chr1:228118785..228120399,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10799456	0.85[EUR][1000 genomes]
rs10799457	0.85[EUR][1000 genomes]
rs10916235	0.89[EUR][1000 genomes]
rs11484724	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12074411	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12078365	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573058	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573059	0.89[EUR][1000 genomes]
rs28376917	0.89[EUR][1000 genomes]
rs28445597	0.89[EUR][1000 genomes]
rs4653525	0.85[EUR][1000 genomes]
rs4653526	0.85[EUR][1000 genomes]
rs4653878	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653880	0.89[EUR][1000 genomes]
rs4653882	0.89[EUR][1000 genomes]
rs4653883	0.84[EUR][1000 genomes]
rs4653885	0.85[EUR][1000 genomes]
rs4653886	0.85[EUR][1000 genomes]
rs6657894	0.88[EUR][1000 genomes]
rs67645046	0.89[EUR][1000 genomes]
rs72752172	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72752178	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72752179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72752184	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72752190	0.85[EUR][1000 genomes]
rs7528139	0.84[EUR][1000 genomes]
rs870305	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
10	nsv873250	chr1:228051234-228121548	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv873251	chr1:228051234-228160911	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10799454	TP53BP2	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228074000-228079400	Weak transcription	HSMM	muscle
2	chr1:228074000-228080200	Weak transcription	Hela-S3	cervix
3	chr1:228074000-228096200	Weak transcription	Gastric	stomach
4	chr1:228074800-228080200	Weak transcription	HMEC	breast
5	chr1:228075200-228079600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:228075600-228079800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:228075600-228080000	Weak transcription	Esophagus	oesophagus
8	chr1:228075600-228109200	Weak transcription	Right Atrium	heart
9	chr1:228075800-228079400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:228075800-228079800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:228076000-228080200	Weak transcription	Fetal Heart	heart
12	chr1:228076000-228083400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:228076000-228094600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:228076200-228080200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:228076400-228079800	Weak transcription	Fetal Stomach	stomach
16	chr1:228076400-228080000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:228076600-228080200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:228076600-228080600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:228076600-228080800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:228077000-228079400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr1:228077200-228079400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:228077400-228080200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:228077600-228079600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:228078000-228080000	Weak transcription	K562	blood
25	chr1:228078000-228080600	Enhancers	Spleen	Spleen
26	chr1:228078200-228081400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:228078400-228079400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:228078400-228080200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:228078400-228081800	Enhancers	Fetal Muscle Leg	muscle
30	chr1:228079000-228079200	Enhancers	Placenta Amnion	Placenta Amnion
31	chr1:228079000-228079400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:228079000-228081000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr1:228079000-228084600	Enhancers	Placenta	Placenta

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