Variant report

Variant	rs1450521
Chromosome Location	chr3:161091237-161091238
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr3:161089095-161091343	MCF-7	breast:	n/a	n/a
2	EP300	chr3:161089035-161091712	MCF-7	breast:	n/a	chr3:161089801-161089817
3	E2F6	chr3:161089363-161091367	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOSL2	chr3:161089080-161091306	MCF-7	breast:	n/a	chr3:161090986-161090995
5	JUND	chr3:161091104-161091242	H1-hESC	embryonic stem cell:	n/a	n/a
6	GABPA	chr3:161089048-161091265	MCF-7	breast:	n/a	n/a
7	ELF1	chr3:161089077-161091484	MCF-7	breast:	n/a	n/a
8	PML	chr3:161089034-161091298	MCF-7	breast:	n/a	n/a
9	TCF12	chr3:161088987-161091243	MCF-7	breast:	n/a	n/a
10	SIN3A	chr3:161089119-161091303	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr3:161089003-161091383	MCF-7	breast:	n/a	chr3:161089343-161089353
12	FOXM1	chr3:161089001-161091338	MCF-7	breast:	n/a	n/a
13	TCF12	chr3:161088830-161091241	MCF-7	breast:	n/a	n/a
14	POLR2A	chr3:161084726-161091997	MCF-7	breast:	n/a	n/a
15	REST	chr3:161089041-161091357	MCF-7	breast:	n/a	n/a
16	MAX	chr3:161089022-161091279	MCF-7	breast:	n/a	chr3:161089343-161089353
17	CEBPB	chr3:161089085-161091543	MCF-7	breast:	n/a	n/a
18	JUND	chr3:161088963-161091603	MCF-7	breast:	n/a	chr3:161090986-161090995
19	TEAD4	chr3:161089112-161091366	MCF-7	breast:	n/a	n/a
20	SIN3AK20	chr3:161088214-161091361	MCF-7	breast:	n/a	n/a
21	PML	chr3:161088156-161091509	MCF-7	breast:	n/a	n/a
22	SRF	chr3:161089046-161091437	MCF-7	breast:	n/a	chr3:161089343-161089353
23	GATA3	chr3:161088834-161091443	MCF-7	breast:	n/a	chr3:161089781-161089790 chr3:161090986-161090996
24	GATA3	chr3:161088930-161091398	MCF-7	breast:	n/a	chr3:161089781-161089790 chr3:161090986-161090996
25	ELF1	chr3:161089164-161091329	MCF-7	breast:	n/a	n/a
26	SIN3AK20	chr3:161088075-161091497	MCF-7	breast:	n/a	n/a
27	NR2F2	chr3:161088681-161091423	MCF-7	breast:	n/a	n/a
28	GATA3	chr3:161089226-161091307	MCF-7	breast:	n/a	chr3:161089781-161089790 chr3:161090986-161090996

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:161089815..161091859-chr5:87970263..87972091,2	MCF-7	breast:
2	chr3:161038392..161046344-chr3:161085640..161093564,25	MCF-7	breast:
3	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
4	chr3:161090661..161092175-chr9:130953250..130955416,2	MCF-7	breast:
5	chr20:45982415..45984680-chr3:161089076..161091449,2	MCF-7	breast:
6	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
7	chr11:75061761..75064404-chr3:161090947..161092751,2	MCF-7	breast:
8	chr3:161090533..161094064-chr8:101963094..101965869,3	MCF-7	breast:
9	chr3:161089431..161091438-chr6:26196434..26199354,2	MCF-7	breast:
10	chr17:57916984..57919121-chr3:161089806..161091709,2	MCF-7	breast:
11	chr3:161089882..161091893-chr9:14313286..14315891,2	MCF-7	breast:
12	chr3:160282384..160284279-chr3:161090070..161092453,3	MCF-7	breast:
13	chr11:65265519..65268230-chr3:161089523..161091817,2	MCF-7	breast:
14	chr3:160813033..160824577-chr3:161083489..161092050,35	MCF-7	breast:
15	chr3:160472518..160475131-chr3:161089184..161091851,3	MCF-7	breast:
16	chr14:38061358..38063507-chr3:161089489..161091930,2	MCF-7	breast:
17	chr21:46347538..46349062-chr3:161090013..161091580,2	MCF-7	breast:
18	chr17:57913968..57916411-chr3:161089503..161091564,2	MCF-7	breast:
19	chr22:30683032..30685513-chr3:161089094..161092006,2	MCF-7	breast:
20	chr20:56282039..56284863-chr3:161089358..161091881,2	MCF-7	breast:
21	chr3:160166836..160169216-chr3:161090028..161092220,2	MCF-7	breast:
22	chr3:161088340..161091318-chr9:131938931..131941651,2	MCF-7	breast:

No data

Variant related genes	Relation type
SPTSSB	TF binding region
ENSG00000129514	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000186432	Chromatin interaction
ENSG00000260572	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000148337	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000245864	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000240138	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000239282	Chromatin interaction
ENSG00000163590	Chromatin interaction
ENSG00000188483	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000204055	Chromatin interaction
ENSG00000147862	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000137486	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000213186	Chromatin interaction
ENSG00000124225	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000229320	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10513564	0.83[EUR][1000 genomes]
rs10936227	0.82[EUR][1000 genomes]
rs11710489	0.88[EUR][1000 genomes]
rs11711695	0.83[EUR][1000 genomes]
rs11715591	0.84[EUR][1000 genomes]
rs11718905	0.83[EUR][1000 genomes]
rs11929238	0.83[EUR][1000 genomes]
rs13059340	0.84[EUR][1000 genomes]
rs13062740	0.82[EUR][1000 genomes]
rs13073147	0.83[EUR][1000 genomes]
rs13076251	0.88[EUR][1000 genomes]
rs13084731	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13084746	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1450519	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1450522	0.86[EUR][1000 genomes]
rs1450523	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1478566	0.82[EUR][1000 genomes]
rs16832082	0.83[EUR][1000 genomes]
rs2054710	0.88[EUR][1000 genomes]
rs2100238	0.83[EUR][1000 genomes]
rs2122527	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404341	0.88[EUR][1000 genomes]
rs2404342	0.88[EUR][1000 genomes]
rs34771618	0.83[EUR][1000 genomes]
rs34896809	0.83[EUR][1000 genomes]
rs35100811	0.86[EUR][1000 genomes]
rs4856701	0.82[EUR][1000 genomes]
rs4856703	0.83[EUR][1000 genomes]
rs60625846	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67460515	0.86[EUR][1000 genomes]
rs6780536	0.83[EUR][1000 genomes]
rs7610985	0.84[EUR][1000 genomes]
rs9844862	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1450521	SPTSSB	cis	Thyroid	GTEx
rs1450521	SPTSSB	cis	Heart Left Ventricle	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161088000-161091400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:161091000-161091800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:161091200-161091400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
4	chr3:161091200-161091400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
5	chr3:161091200-161091400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
6	chr3:161091200-161091400	Enhancers	Brain Germinal Matrix	brain
7	chr3:161091200-161091400	Enhancers	Stomach Mucosa	stomach
8	chr3:161091200-161092800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:161091200-161093200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:161091200-161096800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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