Variant report

Variant	rs13129054
Chromosome Location	chr4:95915991-95915992
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr4:95915823-95916239	A549	lung:	n/a	n/a
2	USF1	chr4:95915945-95916153	SK-N-SH_RA	brain:	n/a	n/a
3	USF1	chr4:95915950-95916248	A549	lung:	n/a	n/a
4	USF2	chr4:95915927-95916171	Hela-S3	cervix:	n/a	chr4:95916063-95916074
5	FOXA1	chr4:95915971-95916134	T-47D	breast:	n/a	n/a
6	USF1	chr4:95915950-95916284	A549	lung:	n/a	n/a
7	USF1	chr4:95915890-95916139	SK-N-SH_RA	brain:	n/a	n/a
8	GATA3	chr4:95915930-95916227	T-47D	breast:	n/a	chr4:95916106-95916114
9	GATA3	chr4:95915987-95916273	MCF-7	breast:	n/a	chr4:95916106-95916114
10	GATA3	chr4:95915652-95916593	MCF-7	breast:	n/a	chr4:95916106-95916114
11	GATA3	chr4:95915947-95916296	T-47D	breast:	n/a	chr4:95916106-95916114
12	ZNF217	chr4:95915964-95916233	MCF-7	breast:	n/a	n/a
13	NR2F2	chr4:95915876-95916359	MCF-7	breast:	n/a	n/a
14	GATA3	chr4:95915921-95916264	MCF-7	breast:	n/a	chr4:95916106-95916114
15	GATA3	chr4:95915893-95916374	MCF-7	breast:	n/a	chr4:95916106-95916114
16	JUND	chr4:95915925-95916469	MCF-7	breast:	n/a	n/a
17	GATA2	chr4:95915946-95916227	SH-SY5Y	brain:	n/a	n/a
18	NR2F2	chr4:95915928-95916348	MCF-7	breast:	n/a	n/a
19	SIN3AK20	chr4:95915808-95916384	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95915803..95916373-chr4:96014810..96015711,2	MCF-7	breast:

Variant related genes	Relation type
BMPR1B	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1023800	0.86[ASN][1000 genomes]
rs1023801	0.86[ASN][1000 genomes]
rs1023802	0.86[ASN][1000 genomes]
rs1023803	0.86[ASN][1000 genomes]
rs1023804	0.86[ASN][1000 genomes]
rs11097454	0.92[ASN][1000 genomes]
rs1154847	0.81[EUR][1000 genomes]
rs1160695	0.88[ASN][1000 genomes]
rs12507710	0.83[ASN][1000 genomes]
rs12508840	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13113714	0.81[ASN][1000 genomes]
rs13128586	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13129062	0.92[ASN][1000 genomes]
rs13145631	0.90[ASN][1000 genomes]
rs1318972	0.86[ASN][1000 genomes]
rs1347346	0.92[ASN][1000 genomes]
rs1373647	0.81[EUR][1000 genomes]
rs1434546	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1434548	0.81[ASN][1000 genomes]
rs1444920	0.92[ASN][1000 genomes]
rs1444921	0.92[ASN][1000 genomes]
rs1444923	0.86[ASN][1000 genomes]
rs1444926	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1469336	0.81[ASN][1000 genomes]
rs1470409	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1530459	0.90[ASN][1000 genomes]
rs1545326	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545327	0.96[ASN][1000 genomes]
rs1545328	0.88[AFR][1000 genomes]
rs1545329	0.92[ASN][1000 genomes]
rs1560909	0.85[ASN][1000 genomes]
rs17022863	0.81[EUR][1000 genomes]
rs1821451	0.88[ASN][1000 genomes]
rs1822826	0.96[ASN][1000 genomes]
rs1822827	0.81[EUR][1000 genomes]
rs1834718	0.85[ASN][1000 genomes]
rs1838501	0.96[ASN][1000 genomes]
rs1867542	0.92[ASN][1000 genomes]
rs2044328	0.86[ASN][1000 genomes]
rs2099996	0.86[ASN][1000 genomes]
rs2120832	0.92[ASN][1000 genomes]
rs2865398	0.81[ASN][1000 genomes]
rs3755874	0.90[ASN][1000 genomes]
rs3775034	0.84[ASN][1000 genomes]
rs3775041	0.89[AFR][1000 genomes]
rs4145993	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4331783	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4397000	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4426786	0.81[ASN][1000 genomes]
rs4450936	0.92[ASN][1000 genomes]
rs4586955	0.81[EUR][1000 genomes]
rs4588466	0.92[ASN][1000 genomes]
rs4699825	0.86[ASN][1000 genomes]
rs4699826	0.86[ASN][1000 genomes]
rs4699827	0.92[ASN][1000 genomes]
rs4699828	0.92[ASN][1000 genomes]
rs58528248	0.81[EUR][1000 genomes]
rs61018424	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6532520	0.90[ASN][1000 genomes]
rs6532522	0.82[AMR][1000 genomes]
rs6532523	0.85[ASN][1000 genomes]
rs6815448	0.92[ASN][1000 genomes]
rs6816059	0.92[ASN][1000 genomes]
rs6820199	0.88[ASN][1000 genomes]
rs6836504	0.92[ASN][1000 genomes]
rs6840826	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6841746	0.92[ASN][1000 genomes]
rs6843668	0.92[ASN][1000 genomes]
rs6844029	0.88[ASN][1000 genomes]
rs6846665	0.84[ASN][1000 genomes]
rs6850046	0.81[EUR][1000 genomes]
rs6853845	0.88[ASN][1000 genomes]
rs6855395	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs716190	0.92[ASN][1000 genomes]
rs723169	0.89[AFR][1000 genomes]
rs723170	0.89[AFR][1000 genomes]
rs7665167	0.83[ASN][1000 genomes]
rs7681859	0.81[EUR][1000 genomes]
rs7698787	0.92[ASN][1000 genomes]
rs895105	0.83[ASN][1000 genomes]
rs920911	0.83[ASN][1000 genomes]
rs920912	0.83[ASN][1000 genomes]
rs965447	0.96[ASN][1000 genomes]
rs973887	0.92[ASN][1000 genomes]
rs996659	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv492312	chr4:95823124-96128327	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv997787	chr4:95859839-95934105	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv537190	chr4:95859839-95934105	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95912600-95916000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr4:95912600-95916600	Weak transcription	Fetal Kidney	kidney
3	chr4:95913400-95916800	Weak transcription	Fetal Thymus	thymus
4	chr4:95915200-95916600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:95915200-95916800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:95915400-95916600	Enhancers	A549	lung
7	chr4:95915400-95916800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:95915400-95916800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr4:95915400-95916800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:95915400-95916800	Enhancers	Thymus	Thymus
11	chr4:95915400-95917000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:95915400-95917000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr4:95915600-95916000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:95915600-95917000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:95915800-95916800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr4:95915800-95916800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:95915800-95916800	Weak transcription	HUVEC	blood vessel

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