Variant report

Variant	rs11735092
Chromosome Location	chr4:88226231-88226232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr4:88225742-88226436	A549	lung:	n/a	n/a
2	GATA3	chr4:88225649-88226546	A549	lung:	n/a	n/a
3	FOSL2	chr4:88225836-88226412	A549	lung:	n/a	n/a
4	TCF7L2	chr4:88225946-88226322	Hela-S3	cervix:	n/a	n/a
5	STAT3	chr4:88225919-88226232	MCF10A-Er-Src	breast:	n/a	n/a
6	BCL3	chr4:88225796-88226325	A549	lung:	n/a	n/a
7	TCF12	chr4:88225534-88226432	MCF-7	breast:	n/a	n/a
8	MAFK	chr4:88225717-88226545	Hela-S3	cervix:	n/a	n/a
9	TCF12	chr4:88225626-88226533	A549	lung:	n/a	n/a
10	RCOR1	chr4:88225763-88226530	Hela-S3	cervix:	n/a	n/a
11	TBP	chr4:88225758-88226310	Hela-S3	cervix:	n/a	n/a
12	ZKSCAN1	chr4:88226184-88226384	Hela-S3	cervix:	n/a	n/a
13	EP300	chr4:88225710-88226451	A549	lung:	n/a	n/a
14	TCF7L2	chr4:88225810-88226302	MCF-7	breast:	n/a	n/a
15	CEBPB	chr4:88225791-88226474	MCF-7	breast:	n/a	n/a
16	GTF2F1	chr4:88225820-88226457	Hela-S3	cervix:	n/a	n/a
17	STAT3	chr4:88225826-88226610	Hela-S3	cervix:	n/a	n/a
18	TCF7L2	chr4:88225796-88226339	PANC-1	pancreas:	n/a	n/a
19	EP300	chr4:88225710-88226470	A549	lung:	n/a	n/a
20	FOXA2	chr4:88225807-88226282	A549	lung:	n/a	n/a
21	KAP1	chr4:88225644-88226391	HEK293	kidney:	n/a	n/a
22	TCF7L2	chr4:88225781-88226283	HEK293	kidney:	n/a	n/a
23	EP300	chr4:88225808-88226277	MCF-7	breast:	n/a	n/a
24	RFX5	chr4:88225679-88226395	Hela-S3	cervix:	n/a	n/a
25	JUND	chr4:88225755-88226399	MCF-7	breast:	n/a	n/a
26	ZNF217	chr4:88225826-88226279	MCF-7	breast:	n/a	n/a
27	REST	chr4:88225751-88226325	A549	lung:	n/a	n/a
28	CEBPB	chr4:88225700-88226496	Hela-S3	cervix:	n/a	n/a
29	FOXM1	chr4:88225661-88226647	MCF-7	breast:	n/a	n/a
30	SIN3AK20	chr4:88225690-88226382	MCF-7	breast:	n/a	n/a
31	SP1	chr4:88225710-88226324	A549	lung:	n/a	n/a
32	EP300	chr4:88225737-88226325	MCF-7	breast:	n/a	n/a
33	BRCA1	chr4:88225715-88226363	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr4:88226162-88226322	Hela-S3	cervix:	n/a	n/a
35	NR2F2	chr4:88225750-88226531	MCF-7	breast:	n/a	n/a
36	EP300	chr4:88225794-88226440	Hela-S3	cervix:	n/a	n/a
37	GATA3	chr4:88225620-88226575	MCF-7	breast:	n/a	n/a
38	SIN3AK20	chr4:88225723-88226306	MCF-7	breast:	n/a	n/a
39	GATA3	chr4:88225597-88226753	MCF-7	breast:	n/a	n/a
40	JUND	chr4:88225763-88226358	Hela-S3	cervix:	n/a	n/a
41	GATA3	chr4:88225730-88226465	A549	lung:	n/a	n/a
42	NR2F2	chr4:88225729-88226274	MCF-7	breast:	n/a	n/a
43	TCF7L2	chr4:88225849-88226390	Hela-S3	cervix:	n/a	n/a
44	SP1	chr4:88225736-88226457	A549	lung:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:88226132..88228278-chr4:88229243..88230944,2	MCF-7	breast:
2	chr4:88224415..88227242-chr4:88231505..88233396,2	K562	blood:
3	chr4:88225790..88227669-chr4:88236912..88239118,2	MCF-7	breast:
4	chr4:88225793..88228433-chr4:88233021..88235909,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR5705	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10001545	0.89[ASN][1000 genomes]
rs10022237	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10084835	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10433879	0.93[ASN][1000 genomes]
rs10433937	0.95[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10440365	0.95[ASN][1000 genomes]
rs11727374	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11935592	0.89[ASN][1000 genomes]
rs13118664	0.89[CHD][hapmap]
rs13130041	0.95[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13130929	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13140105	0.92[ASN][1000 genomes]
rs13142110	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13142655	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13150068	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13150834	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28418877	0.89[ASN][1000 genomes]
rs28419230	0.89[ASN][1000 genomes]
rs28439498	0.87[ASN][1000 genomes]
rs28456144	0.95[ASN][1000 genomes]
rs28528308	0.95[ASN][1000 genomes]
rs28636836	0.88[ASN][1000 genomes]
rs28657030	0.95[ASN][1000 genomes]
rs28664118	0.89[ASN][1000 genomes]
rs28679728	0.89[ASN][1000 genomes]
rs4089	0.95[ASN][1000 genomes]
rs4998663	0.89[ASN][1000 genomes]
rs6531967	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6834488	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6850131	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs6850509	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7663544	0.86[ASN][1000 genomes]
rs7684895	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7694379	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9992651	0.89[CHD][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv516203	chr4:88167878-88228228	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv470050	chr4:88186509-88228228	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	esv2760913	chr4:88194170-88228412	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
8	nsv879527	chr4:88194170-88250203	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
9	esv1802846	chr4:88211056-88246450	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11735092	AFF1	cis	cerebellum	SCAN
rs11735092	SLC10A6	cis	cerebellum	SCAN
rs11735092	DMP1	cis	parietal	SCAN
rs11735092	HSD17B13	cis	parietal	SCAN
rs11735092	CDS1	cis	parietal	SCAN
rs11735092	HSD17B11	cis	parietal	SCAN
rs11735092	HSD17B13	cis	cerebellum	SCAN
rs11735092	GCNT1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88225400-88237800	Strong transcription	Liver	Liver
2	chr4:88225800-88226400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:88225800-88226400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:88225800-88227200	Active TSS	Hela-S3	cervix
5	chr4:88226000-88226600	Active TSS	A549	lung
6	chr4:88226200-88226600	Active TSS	Aorta	Aorta
7	chr4:88226200-88226800	Active TSS	NHEK	skin

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