Variant report

Variant	rs4504703
Chromosome Location	chr9:71394724-71394725
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	ATF1	chr9:71394632-71395101	K562	blood:	n/a	n/a
2	EP300	chr9:71394643-71395431	HepG2	liver:	n/a	n/a
3	TCF12	chr9:71394590-71395239	ECC-1	luminal epithelium:	n/a	n/a
4	PAX5	chr9:71394695-71395090	GM12878	blood:	n/a	n/a
5	RCOR1	chr9:71394439-71395616	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr9:71394334-71395356	H1-hESC	embryonic stem cell:	n/a	n/a
7	NFIC	chr9:71394507-71395603	GM12878	blood:	n/a	n/a
8	TAF1	chr9:71394289-71395205	H1-hESC	embryonic stem cell:	n/a	n/a
9	NRF1	chr9:71394710-71395129	K562	blood:	n/a	chr9:71394932-71394943 chr9:71394952-71394961 chr9:71394932-71394946 chr9:71394950-71394961 chr9:71394934-71394943 chr9:71394947-71394961 chr9:71394932-71394943 chr9:71394950-71394964 chr9:71394950-71394961
10	USF2	chr9:71394340-71394951	Hela-S3	cervix:	n/a	n/a
11	BHLHE40	chr9:71394348-71395445	GM12878	blood:	n/a	n/a
12	BCL3	chr9:71394514-71395083	A549	lung:	n/a	n/a
13	E2F6	chr9:71394419-71395052	H1-hESC	embryonic stem cell:	n/a	chr9:71394933-71394942 chr9:71394951-71394960 chr9:71394905-71394915 chr9:71394588-71394599
14	MAX	chr9:71394645-71395335	A549	lung:	n/a	n/a
15	TAF1	chr9:71394705-71394982	GM12892	blood:	n/a	n/a
16	MAX	chr9:71394349-71395775	NB4	blood:	n/a	n/a
17	MAX	chr9:71394359-71395469	A549	lung:	n/a	n/a
18	ZBTB33	chr9:71394622-71395199	SK-N-SH	brain:	n/a	chr9:71394920-71394935
19	MAX	chr9:71394449-71395505	K562	blood:	n/a	n/a
20	RCOR1	chr9:71394587-71395329	GM12878	blood:	n/a	n/a
21	CHD2	chr9:71394487-71395596	GM12878	blood:	n/a	chr9:71395054-71395064 chr9:71394859-71394869
22	BRCA1	chr9:71394603-71395221	GM12878	blood:	n/a	n/a
23	MAX	chr9:71394317-71395532	K562	blood:	n/a	n/a
24	POLR2A	chr9:71394454-71395596	Gliobla	brain:	n/a	n/a
25	SMC3	chr9:71394599-71395151	HepG2	liver:	n/a	n/a
26	ELF1	chr9:71394419-71395088	K562	blood:	n/a	n/a
27	GTF2F1	chr9:71394411-71395044	K562	blood:	n/a	n/a
28	POLR2A	chr9:71394411-71395332	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr9:71394144-71395603	Raji	blood:	n/a	n/a
30	TCF7L2	chr9:71394463-71395918	Hela-S3	cervix:	n/a	n/a
31	SMC3	chr9:71394558-71395649	Hela-S3	cervix:	n/a	n/a
32	E2F6	chr9:71394355-71395417	K562	blood:	n/a	chr9:71394933-71394942 chr9:71394951-71394960 chr9:71395060-71395069 chr9:71394905-71394915 chr9:71394588-71394599
33	SP4	chr9:71394641-71395173	H1-hESC	embryonic stem cell:	n/a	n/a
34	SIN3AK20	chr9:71394465-71395404	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr9:71394319-71395597	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr9:71394129-71395532	MCF10A-Er-Src	breast:	n/a	n/a
37	FOXA2	chr9:71394640-71395053	A549	lung:	n/a	n/a
38	NRF1	chr9:71394642-71395133	Hela-S3	cervix:	n/a	chr9:71394932-71394943 chr9:71394952-71394961 chr9:71394932-71394946 chr9:71394950-71394961 chr9:71394934-71394943 chr9:71394947-71394961 chr9:71394932-71394943 chr9:71394950-71394964 chr9:71394950-71394961
39	CTCF	chr9:71394709-71395433	GM12878	blood:	n/a	n/a
40	GATA2	chr9:71394444-71395747	SH-SY5Y	brain:	n/a	n/a
41	CHD1	chr9:71394598-71395243	H1-hESC	embryonic stem cell:	n/a	chr9:71395054-71395064 chr9:71394859-71394869
42	ATF3	chr9:71394703-71395104	K562	blood:	n/a	chr9:71394790-71394804
43	NFATC1	chr9:71394432-71395340	GM12878	blood:	n/a	n/a
44	REST	chr9:71394490-71395210	A549	lung:	n/a	n/a
45	MXI1	chr9:71394577-71395622	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr9:71394413-71395437	ECC-1	luminal epithelium:	n/a	n/a
47	STAT1	chr9:71394369-71395323	GM12878	blood:	n/a	n/a
48	GATA1	chr9:71394375-71395933	PBDE	blood:	n/a	n/a
49	POLR2A	chr9:71394485-71395275	HCT-116	colon:	n/a	n/a
50	HEY1	chr9:71394279-71395367	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:71379701..71382544-chr9:71392331..71394766,2	K562	blood:
2	chr16:57570187..57572326-chr9:71393434..71396410,2	MCF-7	breast:
3	chr9:71320021..71321868-chr9:71392573..71394847,2	K562	blood:
4	chr9:71360620..71364939-chr9:71391141..71394857,5	K562	blood:
5	chr9:71319577..71321555-chr9:71393458..71395334,2	MCF-7	breast:
6	chr9:71392487..71395427-chr9:71649569..71651600,2	K562	blood:
7	chr9:71392687..71396802-chr9:71403243..71407898,5	MCF-7	breast:
8	chr9:71357154..71359879-chr9:71394031..71396553,2	MCF-7	breast:

Variant related genes	Relation type
FAM122A	TF binding region
ENSG00000135736	Chromatin interaction
ENSG00000107242	Chromatin interaction
ENSG00000165060	Chromatin interaction
ENSG00000236998	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10511963	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs10869360	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs10869442	0.90[JPT][hapmap]
rs11143607	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11143636	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12350270	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1336492	0.87[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1412986	0.87[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2027204	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs2152647	0.90[JPT][hapmap]
rs4745237	0.85[EUR][1000 genomes]
rs4745268	0.80[EUR][1000 genomes]
rs4745295	0.81[CEU][hapmap]
rs7033278	0.82[CEU][hapmap]
rs7035163	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7853795	0.99[ASN][1000 genomes]
rs7864097	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8114	0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs952589	0.83[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4504703	TJP2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71393800-71394800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:71393800-71395800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:71393800-71395800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr9:71394000-71394800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:71394000-71394800	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr9:71394000-71394800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:71394000-71394800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr9:71394000-71394800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr9:71394000-71394800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:71394000-71394800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr9:71394000-71395600	Active TSS	Brain Anterior Caudate	brain
12	chr9:71394000-71396000	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr9:71394000-71396600	Active TSS	K562	blood
14	chr9:71394200-71394800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr9:71394200-71394800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr9:71394200-71394800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr9:71394200-71394800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr9:71394200-71394800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr9:71394200-71394800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr9:71394200-71394800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:71394200-71394800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:71394200-71394800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr9:71394200-71394800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:71394200-71394800	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr9:71394200-71394800	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr9:71394200-71394800	Flanking Active TSS	Fetal Brain Male	brain
27	chr9:71394200-71394800	Active TSS	Right Atrium	heart
28	chr9:71394200-71394800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr9:71394200-71394800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr9:71394200-71394800	Flanking Active TSS	HMEC	breast
31	chr9:71394200-71394800	Flanking Active TSS	HUVEC	blood vessel
32	chr9:71394200-71394800	Flanking Active TSS	NHEK	skin
33	chr9:71394200-71394800	Flanking Active TSS	NHLF	lung
34	chr9:71394200-71394800	Flanking Active TSS	Osteobl	bone
35	chr9:71394200-71395600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr9:71394200-71395600	Active TSS	Brain Substantia Nigra	brain
37	chr9:71394200-71395600	Active TSS	Fetal Brain Female	brain
38	chr9:71394200-71395600	Active TSS	Thymus	Thymus
39	chr9:71394200-71395800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:71394200-71396000	Active TSS	H9 Cell Line	embryonic stem cell
41	chr9:71394200-71396200	Active TSS	H1 Cell Line	embryonic stem cell
42	chr9:71394200-71396200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr9:71394200-71396200	Active TSS	Fetal Kidney	kidney
44	chr9:71394200-71396400	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr9:71394200-71396400	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr9:71394200-71396800	Active TSS	Psoas Muscle	Psoas
47	chr9:71394400-71394800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr9:71394400-71394800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:71394400-71394800	Flanking Active TSS	Esophagus	oesophagus
50	chr9:71394400-71394800	Flanking Active TSS	Fetal Muscle Trunk	muscle

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