Variant report

Variant	rs4690194
Chromosome Location	chr4:760819-760820
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	POLR2A	chr4:760393-761381	K562	blood:	n/a	n/a
2	POLR2A	chr4:759237-761198	K562	blood:	n/a	n/a
3	POLR2A	chr4:755516-762401	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:759202-761080	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr4:760397-761001	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr4:759233-762364	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:755915-762327	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr4:760409-761375	GM12892	blood:	n/a	n/a
9	POLR2A	chr4:760351-760853	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr4:755285-762979	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr4:760372-761033	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr4:759248-762698	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr4:760511-761110	GM12892	blood:	n/a	n/a
14	POLR2A	chr4:760359-761055	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr4:760609-760918	K562	blood:	n/a	n/a
16	POLR2A	chr4:760409-761067	GM12878	blood:	n/a	n/a
17	NFATC1	chr4:760416-761031	GM12878	blood:	n/a	n/a
18	POLR2A	chr4:756202-761622	HUVEC	blood vessel:	n/a	n/a
19	CCNT2	chr4:759238-761313	K562	blood:	n/a	n/a
20	POLR2A	chr4:759266-762241	K562	blood:	n/a	n/a
21	POLR2A	chr4:753739-764687	K562	blood:	n/a	n/a
22	POLR2A	chr4:759287-761669	K562	blood:	n/a	n/a
23	TEAD4	chr4:760508-760926	K562	blood:	n/a	n/a
24	JUND	chr4:759224-761272	HCT-116	colon:	n/a	chr4:759238-759248 chr4:759239-759247 chr4:759239-759246 chr4:759239-759247 chr4:759237-759248
25	POLR2A	chr4:759089-762357	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr4:759195-761792	HepG2	liver:	n/a	n/a
27	POLR2A	chr4:760352-761342	HCT-116	colon:	n/a	n/a
28	HMGN3	chr4:760751-761001	K562	blood:	n/a	n/a
29	STAT5A	chr4:760353-760861	GM12878	blood:	n/a	n/a
30	POLR2A	chr4:760386-761107	HL-60	blood:	n/a	n/a
31	POLR2A	chr4:759114-761481	PANC-1	pancreas:	n/a	n/a
32	BCL3	chr4:760819-761119	K562	blood:	n/a	n/a
33	POLR2A	chr4:760683-761056	GM12878	blood:	n/a	n/a
34	POLR2A	chr4:760382-761426	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr4:760746-760980	Hela-S3	cervix:	n/a	n/a
36	ZMIZ1	chr4:760551-761033	K562	blood:	n/a	n/a
37	POLR2A	chr4:759145-760857	U87	brain:	n/a	n/a
38	POLR2A	chr4:758129-762123	PFSK-1	brain:	n/a	n/a
39	POLR2A	chr4:760755-760984	A549	lung:	n/a	n/a
40	POLR2A	chr4:760698-761065	A549	lung:	n/a	n/a
41	POLR2A	chr4:760666-761021	HepG2	liver:	n/a	n/a
42	POLR2A	chr4:759225-761044	GM12892	blood:	n/a	n/a
43	POLR2A	chr4:756032-762473	PFSK-1	brain:	n/a	n/a
44	POLR2A	chr4:760485-761025	HepG2	liver:	n/a	n/a
45	POLR2A	chr4:759213-761313	GM19193	blood:	n/a	n/a
46	POLR2A	chr4:756175-762480	GM12891	blood:	n/a	n/a
47	POLR2A	chr4:760753-760989	A549	lung:	n/a	n/a
48	POLR2A	chr4:760333-761384	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr4:760735-760918	A549	lung:	n/a	n/a
50	NFATC1	chr4:759126-761013	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:760680..763356-chr4:818980..821641,2	MCF-7	breast:
2	chr4:758084..763800-chr4:770671..778725,12	MCF-7	breast:
3	chr4:723040..724822-chr4:760521..763494,2	K562	blood:
4	chr4:759810..762809-chr4:1002584..1005442,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233799	TF binding region
ENSG00000127418	Chromatin interaction
ENSG00000249592	Chromatin interaction
ENSG00000168993	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11248040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723514	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11724278	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11725571	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11729160	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11729987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734005	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13127733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17164964	0.85[YRI][hapmap]
rs17165032	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs17165034	0.92[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2242233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733358	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3775143	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4234853	0.85[YRI][hapmap]
rs4690281	1.00[ASW][hapmap];0.85[CEU][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes]
rs4690282	0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4690307	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4690310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4690311	0.93[ASN][1000 genomes]
rs4690312	0.92[ASN][1000 genomes]
rs4690315	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57170954	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59438465	0.91[AFR][1000 genomes]
rs60018246	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73207757	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7682244	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs899391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs899393	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
5	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
9	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
10	nsv829834	chr4:665477-775524	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv878253	chr4:708932-771587	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	nsv878254	chr4:708932-899143	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv878255	chr4:708932-1052488	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
14	nsv878257	chr4:712222-852313	Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv878258	chr4:712222-1058358	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
16	nsv878259	chr4:713920-852313	Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
17	nsv878260	chr4:713920-1052488	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv4195	chr4:727187-768059	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
19	nsv818207	chr4:753944-821490	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
20	nsv878261	chr4:756686-1047794	Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
21	nsv1007928	chr4:757263-813885	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
22	nsv520136	chr4:759709-780883	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers 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 target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4690194	PCGF3	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:727000-767600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:728600-763400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr4:729000-762600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr4:742600-763600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr4:742800-764000	Weak transcription	Small Intestine	intestine
6	chr4:744400-763400	Weak transcription	Right Atrium	heart
7	chr4:746000-773800	Weak transcription	Fetal Brain Male	brain
8	chr4:748200-763400	Weak transcription	Brain Substantia Nigra	brain
9	chr4:753600-769000	ZNF genes & repeats	Fetal Stomach	stomach
10	chr4:753600-773800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:753800-761000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:753800-761000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:753800-761400	Strong transcription	Colonic Mucosa	Colon
14	chr4:753800-764200	ZNF genes & repeats	Aorta	Aorta
15	chr4:753800-764600	Strong transcription	Fetal Muscle Leg	muscle
16	chr4:753800-764800	Strong transcription	Fetal Lung	lung
17	chr4:753800-765400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:753800-766600	Strong transcription	Dnd41	blood
19	chr4:753800-768000	Strong transcription	Thymus	Thymus
20	chr4:753800-768400	Strong transcription	Primary T cells from cord blood	blood
21	chr4:753800-771600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr4:753800-773200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:753800-773200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:753800-773400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:753800-773400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:754000-761400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:754000-764000	Strong transcription	Fetal Brain Female	brain
28	chr4:754000-771600	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr4:754000-773600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:754200-765200	Strong transcription	Ovary	ovary
31	chr4:754200-765600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr4:754200-765600	Strong transcription	Gastric	stomach
33	chr4:754200-771600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr4:754400-764400	Strong transcription	Rectal Smooth Muscle	rectum
35	chr4:754400-765400	Strong transcription	Primary hematopoietic stem cells	blood
36	chr4:754400-765400	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:754400-765600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr4:754400-765600	Strong transcription	HUVEC	blood vessel
39	chr4:754400-773400	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr4:754600-762800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr4:754600-763400	Weak transcription	Fetal Heart	heart
42	chr4:754600-765000	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:754600-765200	Weak transcription	Psoas Muscle	Psoas
44	chr4:755200-764200	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:755600-763400	Weak transcription	HSMMtube	muscle
46	chr4:755600-774200	Weak transcription	Hela-S3	cervix
47	chr4:756400-762800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:756400-764800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr4:756600-766800	Strong transcription	Stomach Smooth Muscle	stomach
50	chr4:756800-761200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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