Variant report

Variant	rs9985747
Chromosome Location	chr4:657366-657367
allele	A/G
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	chr4:657209-658164	GM15510	blood:	n/a	n/a
2	MAX	chr4:657274-658234	H1-hESC	embryonic stem cell:	n/a	chr4:657449-657459
3	SP1	chr4:657293-657709	GM12878	blood:	n/a	chr4:657428-657440 chr4:657487-657499 chr4:657448-657460 chr4:657484-657498 chr4:657448-657460 chr4:657489-657498 chr4:657488-657497 chr4:657428-657440 chr4:657487-657499 chr4:657449-657458 chr4:657488-657498 chr4:657489-657498
4	POLR2A	chr4:657356-658182	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:657340-657682	GM12891	blood:	n/a	n/a
6	EGR1	chr4:657272-657524	K562	blood:	n/a	chr4:657499-657509 chr4:657453-657462 chr4:657450-657463 chr4:657450-657464 chr4:657450-657463 chr4:657449-657464 chr4:657450-657463 chr4:657429-657439 chr4:657451-657465 chr4:657450-657463
7	POLR2A	chr4:657339-658233	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:657234-658353	H1-hESC	embryonic stem cell:	n/a	n/a
9	MXI1	chr4:656777-658347	SK-N-SH	brain:	n/a	n/a
10	MAX	chr4:657228-658269	H1-hESC	embryonic stem cell:	n/a	chr4:657449-657459
11	POLR2A	chr4:657261-658246	GM12891	blood:	n/a	n/a
12	POLR2A	chr4:657244-658126	GM18951	blood:	n/a	n/a
13	ZBTB7A	chr4:657191-657926	ECC-1	luminal epithelium:	n/a	chr4:657487-657494
14	GABPA	chr4:657227-658172	H1-hESC	embryonic stem cell:	n/a	chr4:658017-658026
15	EGR1	chr4:657364-657554	K562	blood:	n/a	chr4:657499-657509 chr4:657453-657462 chr4:657450-657463 chr4:657450-657464 chr4:657450-657463 chr4:657449-657464 chr4:657450-657463 chr4:657429-657439 chr4:657451-657465 chr4:657450-657463
16	POLR2A	chr4:657300-657736	H1-hESC	embryonic stem cell:	n/a	n/a
17	EGR1	chr4:657328-657565	GM12878	blood:	n/a	chr4:657499-657509 chr4:657453-657462 chr4:657450-657463 chr4:657450-657464 chr4:657450-657463 chr4:657449-657464 chr4:657450-657463 chr4:657429-657439 chr4:657451-657465 chr4:657450-657463
18	E2F6	chr4:657344-658305	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr4:657079-658351	GM12878	blood:	n/a	n/a
20	POLR2A	chr4:657210-658217	GM18526	blood:	n/a	n/a
21	EGR1	chr4:657304-657582	GM12878	blood:	n/a	chr4:657499-657509 chr4:657453-657462 chr4:657450-657463 chr4:657450-657464 chr4:657450-657463 chr4:657449-657464 chr4:657450-657463 chr4:657429-657439 chr4:657451-657465 chr4:657450-657463
22	POLR2A	chr4:657165-657664	SK-N-SH	brain:	n/a	n/a
23	YY1	chr4:657265-657797	HepG2	liver:	n/a	chr4:657452-657461 chr4:657446-657460
24	EGR1	chr4:657212-657703	H1-hESC	embryonic stem cell:	n/a	chr4:657499-657509 chr4:657453-657462 chr4:657450-657463 chr4:657450-657464 chr4:657450-657463 chr4:657449-657464 chr4:657450-657463 chr4:657429-657439 chr4:657451-657465 chr4:657450-657463
25	ZBTB7A	chr4:657215-658107	ECC-1	luminal epithelium:	n/a	chr4:657487-657494
26	GABPA	chr4:657279-658371	SK-N-SH	brain:	n/a	chr4:658017-658026
27	POLR2A	chr4:657205-658301	Raji	blood:	n/a	n/a
28	BHLHE40	chr4:657291-658227	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:657056-657858	SK-N-MC	brain:	n/a	n/a
30	EBF1	chr4:657254-657692	GM12878	blood:	n/a	n/a
31	USF1	chr4:657275-658143	H1-hESC	embryonic stem cell:	n/a	chr4:657598-657609
32	MAZ	chr4:657310-658193	GM12878	blood:	n/a	chr4:657449-657459
33	SIN3AK20	chr4:657319-657806	PANC-1	pancreas:	n/a	n/a
34	EGR1	chr4:657267-657673	ECC-1	luminal epithelium:	n/a	chr4:657499-657509 chr4:657453-657462 chr4:657450-657463 chr4:657450-657464 chr4:657450-657463 chr4:657449-657464 chr4:657450-657463 chr4:657429-657439 chr4:657451-657465 chr4:657450-657463
35	POLR2A	chr4:657362-658167	GM19193	blood:	n/a	n/a
36	E2F6	chr4:657230-658395	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr4:657325-657714	PBDE	blood:	n/a	n/a
38	POLR2A	chr4:657298-658190	GM12878	blood:	n/a	n/a
39	POLR2A	chr4:657254-657720	GM19099	blood:	n/a	n/a
40	POLR2A	chr4:657184-658258	GM12878	blood:	n/a	n/a
41	POLR2A	chr4:657333-657725	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr4:657181-658244	GM12878	blood:	n/a	n/a
43	ZEB1	chr4:657279-658072	GM12878	blood:	n/a	n/a
44	CTCF	chr4:657300-657419	Spleen_OC	spleen:	n/a	chr4:657372-657381
45	SP4	chr4:657356-657744	H1-hESC	embryonic stem cell:	n/a	chr4:657485-657501 chr4:657483-657499 chr4:657450-657466
46	ZNF143	chr4:657360-657572	GM12878	blood:	n/a	n/a
47	SIN3A	chr4:657346-658200	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr4:657354-657904	MCF-7	breast:	n/a	n/a
49	ELF1	chr4:657030-658394	GM12878	blood:	n/a	n/a
50	TCF3	chr4:657353-657686	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:646849..649113-chr4:654761..657491,3	K562	blood:
2	chr4:644054..646414-chr4:656838..659721,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATP5I-5	chr4:657116-657999	NONHSAT094591

Variant related genes	Relation type
ENSG00000272927	TF binding region
PDE6B	TF binding region
ENSG00000242686	Chromatin interaction
ENSG00000133256	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10027549	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10030136	0.81[EUR][1000 genomes]
rs28407346	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28470912	0.81[EUR][1000 genomes]
rs28483373	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28488910	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28525003	0.81[EUR][1000 genomes]
rs28569875	0.85[EUR][1000 genomes]
rs28573204	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28586910	0.84[AMR][1000 genomes]
rs28742266	0.83[EUR][1000 genomes]
rs3864131	0.83[EUR][1000 genomes]
rs3891250	0.80[AMR][1000 genomes]
rs4463020	0.81[EUR][1000 genomes]
rs58227539	0.81[EUR][1000 genomes]
rs73056602	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73058406	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7436737	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	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
9	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv878248	chr4:645300-685993	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
16	nsv878249	chr4:649639-691026	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9985747	RP11-1191J2.2	cis	Thyroid	GTEx
rs9985747	RP11-1191J2.2	cis	lung	GTEx
rs9985747	RP11-1191J2.2	cis	Nerve Tibial	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:656600-657400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:656600-657400	Flanking Active TSS	Brain Germinal Matrix	brain
3	chr4:656800-657400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr4:656800-657400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr4:656800-657400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr4:656800-657400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr4:656800-657400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr4:656800-657400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr4:656800-657400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:656800-657400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr4:656800-657400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:656800-657400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:656800-657400	Active TSS	Brain Anterior Caudate	brain
14	chr4:656800-657400	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr4:656800-657400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr4:656800-657400	Flanking Active TSS	Fetal Intestine Small	intestine
17	chr4:656800-657400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
18	chr4:656800-657400	Flanking Active TSS	Fetal Thymus	thymus
19	chr4:656800-657400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
20	chr4:656800-657600	Flanking Active TSS	Fetal Brain Female	brain
21	chr4:656800-657600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
22	chr4:656800-658200	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr4:656800-658200	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr4:656800-658200	Flanking Active TSS	Pancreas	Pancrea
25	chr4:656800-658400	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr4:656800-658400	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr4:656800-658400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr4:656800-658400	Active TSS	Fetal Intestine Large	intestine
29	chr4:656800-658800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:657000-657400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:657000-657400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr4:657000-657400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr4:657000-657400	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr4:657000-657400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:657000-657400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr4:657000-657400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:657000-657400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr4:657000-657400	Flanking Active TSS	Brain Angular Gyrus	brain
39	chr4:657000-657400	Flanking Active TSS	Fetal Stomach	stomach
40	chr4:657000-657400	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr4:657000-657400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
42	chr4:657000-657400	Flanking Active TSS	Thymus	Thymus
43	chr4:657000-657400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr4:657000-657600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:657000-657600	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr4:657000-657600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
47	chr4:657000-657600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr4:657000-657600	Flanking Active TSS	Lung	lung
49	chr4:657000-657600	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
50	chr4:657000-657800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin

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