Variant report

Variant	rs12153073
Chromosome Location	chr5:75475022-75475023
allele	C/T
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	NFIC	chr5:75474553-75475370	GM12878	blood:	n/a	n/a
2	ATF2	chr5:75474650-75475133	GM12878	blood:	n/a	n/a
3	RUNX3	chr5:75474625-75475176	GM12878	blood:	n/a	n/a
4	FOXM1	chr5:75474577-75475208	GM12878	blood:	n/a	n/a
5	BATF	chr5:75474748-75475148	GM12878	blood:	n/a	n/a
6	MTA3	chr5:75474665-75475143	GM12878	blood:	n/a	n/a
7	STAT5A	chr5:75474723-75475093	GM12878	blood:	n/a	n/a
8	PML	chr5:75474596-75475225	GM12878	blood:	n/a	n/a
9	BCL3	chr5:75474685-75475133	GM12878	blood:	n/a	n/a
10	NFATC1	chr5:75474670-75475067	GM12878	blood:	n/a	n/a
11	ATF2	chr5:75474597-75475178	GM12878	blood:	n/a	n/a
12	EP300	chr5:75474006-75476352	SK-N-SH	brain:	n/a	chr5:75474206-75474220 chr5:75474895-75474909
13	EP300	chr5:75474763-75475098	GM12878	blood:	n/a	chr5:75474895-75474909
14	BCL11A	chr5:75474738-75475112	GM12878	blood:	n/a	n/a
15	RUNX3	chr5:75474756-75475139	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75011937..75013471-chr5:75474552..75477211,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254893	TF binding region
ENSG00000152359	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10038253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10040232	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10064352	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10474464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742697	0.87[ASN][1000 genomes]
rs12152728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13153946	0.87[ASN][1000 genomes]
rs13158110	0.87[ASN][1000 genomes]
rs13174339	0.87[ASN][1000 genomes]
rs13178459	0.87[ASN][1000 genomes]
rs1553324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17651115	0.87[ASN][1000 genomes]
rs34476924	1.00[ASN][1000 genomes]
rs35357454	0.81[ASN][1000 genomes]
rs4532342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4582256	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703696	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704283	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704286	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58628146	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62361382	0.87[ASN][1000 genomes]
rs62363488	0.87[ASN][1000 genomes]
rs62363490	0.87[ASN][1000 genomes]
rs6414967	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414968	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453205	0.87[ASN][1000 genomes]
rs6453206	0.87[ASN][1000 genomes]
rs6453208	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6859434	0.87[ASN][1000 genomes]
rs6866404	0.87[ASN][1000 genomes]
rs6881418	0.87[ASN][1000 genomes]
rs72771998	0.81[ASN][1000 genomes]
rs736005	0.87[ASN][1000 genomes]
rs7710307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732173	1.00[ASN][1000 genomes]
rs7732692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734441	0.81[ASN][1000 genomes]
rs9293675	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1033350	chr5:75367809-75538460	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1034853	chr5:75382047-75534981	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv462212	chr5:75388834-75534570	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv598676	chr5:75388834-75534570	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv526084	chr5:75410511-75530494	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75470600-75476400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:75471800-75477000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:75472400-75477000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:75472600-75475800	Enhancers	GM12878-XiMat	blood
5	chr5:75472600-75476200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:75472600-75476800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr5:75472600-75477000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr5:75472600-75477000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:75472800-75476400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:75472800-75476600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr5:75472800-75476600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:75472800-75476800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:75472800-75477000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:75473200-75475400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr5:75474000-75475400	Weak transcription	Placenta	Placenta
16	chr5:75474200-75475400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr5:75474200-75475400	Weak transcription	K562	blood
18	chr5:75474200-75475400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr5:75474200-75476600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:75475000-75476200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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