Variant report

Variant	rs10939653
Chromosome Location	chr4:16198439-16198440
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	CTCF	chr4:16198101-16198484	GM12878	blood:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
2	RAD21	chr4:16198114-16198498	H1-hESC	embryonic stem cell:	n/a	chr4:16198433-16198442
3	CTCF	chr4:16198072-16198514	MCF-7	breast:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
4	JUND	chr4:16198015-16198524	T-47D	breast:	n/a	n/a
5	ZNF143	chr4:16198174-16198467	GM12878	blood:	n/a	n/a
6	RAD21	chr4:16198112-16198549	A549	lung:	n/a	chr4:16198433-16198442
7	RUNX3	chr4:16198029-16198500	GM12878	blood:	n/a	n/a
8	FOXA1	chr4:16198001-16198463	T-47D	breast:	n/a	n/a
9	CTCF	chr4:16198101-16198464	ECC-1	luminal epithelium:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
10	EP300	chr4:16197977-16198518	T-47D	breast:	n/a	chr4:16198211-16198221 chr4:16198357-16198371 chr4:16198507-16198516 chr4:16198361-16198375
11	POLR2A	chr4:16198249-16198626	MCF10A-Er-Src	breast:	n/a	n/a
12	SPI1	chr4:16198184-16198494	GM12878	blood:	n/a	n/a
13	SPI1	chr4:16197886-16198631	GM12878	blood:	n/a	chr4:16198505-16198518
14	CTCF	chr4:16198054-16198490	T-47D	breast:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
15	CTCF	chr4:16197997-16198580	MCF-7	breast:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
16	CTCF	chr4:16197961-16198728	HCT-116	colon:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
17	TEAD4	chr4:16198031-16198594	ECC-1	luminal epithelium:	n/a	n/a
18	CTCF	chr4:16198029-16198634	HCT-116	colon:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
19	CTCF	chr4:16198114-16198471	A549	lung:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
20	RAD21	chr4:16198058-16198524	H1-hESC	embryonic stem cell:	n/a	chr4:16198433-16198442
21	CTCF	chr4:16198170-16198485	ECC-1	luminal epithelium:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
22	CTCF	chr4:16198151-16198512	Spleen_OC	spleen:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
23	CTCF	chr4:16198300-16198450	NHLF	lung:	n/a	n/a
24	JUND	chr4:16198172-16198457	H1-hESC	embryonic stem cell:	n/a	n/a
25	RAD21	chr4:16198104-16198466	IMR90	lung:	n/a	chr4:16198433-16198442
26	MYC	chr4:16198179-16198556	MCF10A-Er-Src	breast:	n/a	n/a
27	FOXA2	chr4:16198120-16198459	A549	lung:	n/a	n/a
28	RAD21	chr4:16198019-16198499	HCT-116	colon:	n/a	chr4:16198433-16198442
29	CTCF	chr4:16198121-16198482	Medullo	brain:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
30	RAD21	chr4:16198085-16198546	ECC-1	luminal epithelium:	n/a	chr4:16198433-16198442
31	TEAD4	chr4:16198088-16198563	ECC-1	luminal epithelium:	n/a	n/a
32	ZNF143	chr4:16198159-16198465	H1-hESC	embryonic stem cell:	n/a	n/a
33	RUNX3	chr4:16198162-16198452	GM12878	blood:	n/a	n/a
34	ELF1	chr4:16198185-16198559	MCF-7	breast:	n/a	n/a
35	POLR2A	chr4:16198229-16198490	U87	brain:	n/a	n/a
36	RAD21	chr4:16197997-16198570	MCF-7	breast:	n/a	chr4:16198433-16198442
37	CEBPB	chr4:16198348-16198846	IMR90	lung:	n/a	n/a
38	SPI1	chr4:16198051-16198563	GM12891	blood:	n/a	chr4:16198505-16198518
39	GATA3	chr4:16198124-16198548	T-47D	breast:	n/a	n/a
40	RAD21	chr4:16198090-16198564	A549	lung:	n/a	chr4:16198433-16198442
41	TEAD4	chr4:16198082-16198517	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr4:16197947-16198653	A549	lung:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
43	RAD21	chr4:16198002-16198667	HCT-116	colon:	n/a	chr4:16198433-16198442
44	CTCF	chr4:16198165-16198453	MCF-7	breast:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
45	SPI1	chr4:16198177-16198514	GM12891	blood:	n/a	n/a
46	ZC3H11A	chr4:16198275-16198467	K562	blood:	n/a	n/a
47	CTCF	chr4:16198105-16198513	IMR90	lung:	n/a	chr4:16198179-16198197 chr4:16198174-16198195
48	RAD21	chr4:16198111-16198484	H1-hESC	embryonic stem cell:	n/a	chr4:16198433-16198442
49	TEAD4	chr4:16198024-16198569	H1-hESC	embryonic stem cell:	n/a	n/a
50	STAT3	chr4:16198194-16198440	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
TAPT1	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10019399	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs10034719	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10516298	0.97[CHD][hapmap];0.87[JPT][hapmap]
rs10516299	0.96[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10939652	0.85[ASN][1000 genomes]
rs11724076	0.81[ASN][1000 genomes]
rs11731602	0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11736424	0.81[ASN][1000 genomes]
rs11736827	0.81[ASN][1000 genomes]
rs12504884	0.81[ASN][1000 genomes]
rs12506249	0.94[ASN][1000 genomes]
rs12506478	0.81[ASN][1000 genomes]
rs12513244	0.81[ASN][1000 genomes]
rs12651110	0.84[ASN][1000 genomes]
rs1373112	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.99[ASN][1000 genomes]
rs1662654	0.87[CHD][hapmap]
rs1662656	0.82[ASN][1000 genomes]
rs16893138	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16893143	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs16893144	0.86[JPT][hapmap]
rs16893147	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs16893158	0.97[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs178450	0.81[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs28453363	0.81[ASN][1000 genomes]
rs28618674	0.81[ASN][1000 genomes]
rs28645901	0.94[ASN][1000 genomes]
rs317869	0.81[CHB][hapmap];0.87[CHD][hapmap];0.84[ASN][1000 genomes]
rs317870	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs317871	0.81[ASN][1000 genomes]
rs317872	0.81[ASN][1000 genomes]
rs317874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs317875	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs317878	0.81[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs35851218	0.81[ASN][1000 genomes]
rs56023844	0.84[ASN][1000 genomes]
rs56218994	0.85[ASN][1000 genomes]
rs57089965	0.83[ASN][1000 genomes]
rs60460559	0.81[ASN][1000 genomes]
rs60768295	0.81[ASN][1000 genomes]
rs73128457	0.83[ASN][1000 genomes]
rs73130433	0.83[ASN][1000 genomes]
rs73130439	0.83[ASN][1000 genomes]
rs73130445	0.83[ASN][1000 genomes]
rs73130449	0.84[ASN][1000 genomes]
rs73130451	0.84[ASN][1000 genomes]
rs73130453	0.84[ASN][1000 genomes]
rs73130456	0.81[ASN][1000 genomes]
rs7657191	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs894639	0.89[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.88[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	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10939653	FLJ39653	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16168000-16208000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:16168000-16213800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:16170800-16208000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:16171400-16207200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:16181200-16223800	Weak transcription	Fetal Brain Male	brain
6	chr4:16184200-16200600	Strong transcription	Fetal Thymus	thymus
7	chr4:16187400-16199600	Weak transcription	Hela-S3	cervix
8	chr4:16191400-16207000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:16192200-16204800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:16193000-16205000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr4:16193000-16207600	Weak transcription	Brain Germinal Matrix	brain
12	chr4:16193000-16208200	Weak transcription	Esophagus	oesophagus
13	chr4:16193000-16216000	Weak transcription	Spleen	Spleen
14	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon
15	chr4:16193200-16205800	Weak transcription	Fetal Intestine Small	intestine
16	chr4:16193200-16206800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:16193200-16207000	Weak transcription	Pancreas	Pancrea
18	chr4:16193200-16208000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:16193200-16208000	Weak transcription	Lung	lung
20	chr4:16193200-16225800	Weak transcription	Fetal Brain Female	brain
21	chr4:16193400-16211200	Weak transcription	Placenta	Placenta
22	chr4:16193600-16203000	Weak transcription	HepG2	liver
23	chr4:16193600-16208600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:16193800-16198800	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr4:16193800-16206400	Weak transcription	K562	blood
26	chr4:16194200-16202400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr4:16195000-16204800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:16195400-16199600	Weak transcription	Right Ventricle	heart
29	chr4:16195400-16199600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:16195400-16199600	Weak transcription	Small Intestine	intestine
31	chr4:16195400-16201400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr4:16195400-16201400	Weak transcription	Left Ventricle	heart
33	chr4:16195400-16201600	Weak transcription	Thymus	Thymus
34	chr4:16195400-16203200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr4:16195400-16207000	Weak transcription	Gastric	stomach
36	chr4:16196200-16198600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:16196200-16201400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:16196200-16203400	Weak transcription	Fetal Muscle Leg	muscle
39	chr4:16196200-16207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:16196600-16198600	Enhancers	Fetal Heart	heart
41	chr4:16197000-16199000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr4:16197200-16199200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr4:16197400-16198800	Strong transcription	Dnd41	blood
44	chr4:16197400-16200800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:16197600-16199200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
46	chr4:16197800-16198800	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr4:16197800-16199000	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr4:16197800-16199000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:16197800-16199200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:16197800-16199200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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