Variant report

Variant	rs10499405
Chromosome Location	chr7:11791774-11791775
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	FOXA2	chr7:11791403-11792120	A549	lung:	n/a	n/a
2	FOSL2	chr7:11790835-11791966	A549	lung:	n/a	chr7:11791126-11791134
3	EP300	chr7:11790865-11792180	A549	lung:	n/a	chr7:11791071-11791085
4	NR3C1	chr7:11791532-11792077	A549	lung:	n/a	n/a
5	NR3C1	chr7:11791436-11792077	A549	lung:	n/a	n/a
6	TCF7L2	chr7:11791026-11792212	PANC-1	pancreas:	n/a	n/a
7	GATA3	chr7:11790758-11792156	A549	lung:	n/a	n/a
8	MAX	chr7:11790782-11792116	A549	lung:	n/a	chr7:11791320-11791329
9	GATA3	chr7:11791540-11792063	MCF-7	breast:	n/a	n/a
10	NR3C1	chr7:11791520-11791986	A549	lung:	n/a	n/a
11	TCF12	chr7:11791375-11791958	A549	lung:	n/a	chr7:11791736-11791743
12	NR3C1	chr7:11790859-11792173	A549	lung:	n/a	chr7:11791125-11791134 chr7:11791126-11791135
13	JUND	chr7:11791459-11792011	A549	lung:	n/a	n/a
14	POLR2A	chr7:11791387-11792058	PANC-1	pancreas:	n/a	n/a
15	TEAD4	chr7:11791499-11792002	A549	lung:	n/a	n/a
16	FOXA1	chr7:11791555-11791984	T-47D	breast:	n/a	n/a
17	NR3C1	chr7:11791481-11792051	A549	lung:	n/a	n/a
18	GATA3	chr7:11790958-11792108	A549	lung:	n/a	n/a
19	FOXA2	chr7:11791223-11792188	A549	lung:	n/a	n/a
20	SP1	chr7:11790901-11792119	A549	lung:	n/a	chr7:11791034-11791046 chr7:11791034-11791046
21	REST	chr7:11790973-11792042	A549	lung:	n/a	n/a
22	GATA3	chr7:11791565-11791961	T-47D	breast:	n/a	n/a
23	SP1	chr7:11790800-11792218	A549	lung:	n/a	chr7:11791034-11791046 chr7:11791034-11791046
24	USF1	chr7:11791538-11791944	A549	lung:	n/a	n/a
25	EP300	chr7:11790460-11792207	A549	lung:	n/a	chr7:11791071-11791085
26	BCL3	chr7:11790859-11792070	A549	lung:	n/a	n/a
27	NR2F2	chr7:11791525-11791935	MCF-7	breast:	n/a	n/a
28	TCF12	chr7:11790726-11792272	A549	lung:	n/a	chr7:11791736-11791743
29	NR3C1	chr7:11791503-11792026	A549	lung:	n/a	n/a
30	BCL3	chr7:11791136-11792059	A549	lung:	n/a	n/a
31	NR2F2	chr7:11791569-11792034	MCF-7	breast:	n/a	n/a
32	CREB1	chr7:11791682-11791955	A549	lung:	n/a	n/a
33	POLR2A	chr7:11791437-11792012	PANC-1	pancreas:	n/a	n/a
34	NR3C1	chr7:11791632-11791962	A549	lung:	n/a	n/a
35	FOXA1	chr7:11791597-11791897	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
THSD7A	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10265139	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10276715	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10950366	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12667493	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12667512	1.00[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12671899	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1465007	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1465008	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1467344	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1467345	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1526521	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1526522	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1526532	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1526533	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1526555	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1534234	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17165146	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17165147	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17165166	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17165172	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17165181	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2355076	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2355077	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4236265	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4506091	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4721008	0.87[EUR][1000 genomes]
rs4721010	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55786242	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55860284	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56310669	0.95[EUR][1000 genomes]
rs56835192	0.96[EUR][1000 genomes]
rs57645050	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58747700	0.92[EUR][1000 genomes]
rs60211624	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6460838	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6460839	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66741322	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66784951	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66791240	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67195807	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67255535	0.92[EUR][1000 genomes]
rs67388503	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67907409	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs68076870	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6957349	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6960116	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6973826	1.00[CEU][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes]
rs6973931	1.00[CEU][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73057039	0.92[EUR][1000 genomes]
rs73298449	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7788213	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7795628	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7802597	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9691513	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9691520	1.00[CEU][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs999879	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs999880	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[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	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv887612	chr7:11756776-11806289	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv887613	chr7:11766964-11806289	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv887614	chr7:11778424-12211198	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv970796	chr7:11787992-11794418	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
6	nsv525415	chr7:11791621-11795598	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10499405	ETV1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:11783000-11793000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr7:11790400-11791800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:11790600-11792600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:11791600-11791800	Active TSS	A549	lung
5	chr7:11791600-11792000	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr7:11791600-11792200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr7:11791600-11795000	Weak transcription	Placenta	Placenta

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