Variant report

Variant	rs56177309
Chromosome Location	chr4:7803825-7803826
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	RAD21	chr4:7803707-7804331	HCT-116	colon:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
2	RAD21	chr4:7803783-7804333	A549	lung:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
3	SMC3	chr4:7803649-7804354	SK-N-SH	brain:	n/a	chr4:7804038-7804052
4	JUND	chr4:7803824-7804195	K562	blood:	n/a	chr4:7803890-7803899
5	CTCF	chr4:7803801-7804281	GM12878	blood:	n/a	chr4:7804031-7804052 chr4:7804037-7804053 chr4:7804036-7804054
6	CTCF	chr4:7803816-7804264	HepG2	liver:	n/a	chr4:7804031-7804052 chr4:7804037-7804053 chr4:7804036-7804054
7	CTCF	chr4:7803723-7804440	SK-N-SH	brain:	n/a	chr4:7804031-7804052 chr4:7804037-7804053 chr4:7804036-7804054
8	ATF2	chr4:7803628-7804231	GM12878	blood:	n/a	n/a
9	RAD21	chr4:7803759-7804345	A549	lung:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
10	CTCF	chr4:7803790-7804272	IMR90	lung:	n/a	chr4:7804031-7804052 chr4:7804037-7804053 chr4:7804036-7804054
11	RAD21	chr4:7803788-7804248	MCF-7	breast:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
12	CTCF	chr4:7803820-7803970	HFF-Myc	foreskin:	n/a	n/a
13	JUN	chr4:7803762-7804172	HepG2	liver:	n/a	chr4:7803890-7803899 chr4:7803886-7803899
14	CTCF	chr4:7803795-7804321	MCF-7	breast:	n/a	chr4:7804031-7804052 chr4:7804037-7804053 chr4:7804036-7804054
15	CTCF	chr4:7803800-7803950	HFF	foreskin:	n/a	n/a
16	RAD21	chr4:7803811-7804218	GM12878	blood:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
17	RAD21	chr4:7803724-7804343	MCF-7	breast:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
18	RAD21	chr4:7803666-7804381	HCT-116	colon:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
19	CTCF	chr4:7803820-7803970	HCM	heart:	n/a	n/a
20	SMC3	chr4:7803781-7804239	GM12878	blood:	n/a	chr4:7804038-7804052
21	RAD21	chr4:7803731-7804288	HepG2	liver:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
22	CTCF	chr4:7803780-7803930	HAc	cerebellar:	n/a	n/a
23	MAZ	chr4:7803494-7804371	IMR90	lung:	n/a	n/a
24	BRCA1	chr4:7803812-7804123	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr4:7803792-7804206	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr4:7803672-7804359	A549	lung:	n/a	chr4:7804031-7804052 chr4:7804037-7804053 chr4:7804036-7804054
27	RAD21	chr4:7803247-7804417	SK-N-SH	brain:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
28	RAD21	chr4:7803811-7804312	H1-hESC	embryonic stem cell:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
29	RAD21	chr4:7803798-7804226	SK-N-SH_RA	brain:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
30	CTCF	chr4:7803821-7804219	MCF-7	breast:	n/a	chr4:7804031-7804052 chr4:7804037-7804053 chr4:7804036-7804054
31	RAD21	chr4:7803786-7804249	GM12878	blood:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
32	CTCF	chr4:7803768-7804183	A549	lung:	n/a	chr4:7804031-7804052 chr4:7804037-7804053 chr4:7804036-7804054
33	RAD21	chr4:7803817-7804277	SK-N-SH_RA	brain:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
34	CTCF	chr4:7803800-7803950	WI-38	lung:	n/a	n/a
35	POLR2A	chr4:7803766-7804265	PANC-1	pancreas:	n/a	n/a
36	RAD21	chr4:7803747-7804293	ECC-1	luminal epithelium:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
37	RFX5	chr4:7803806-7804092	K562	blood:	n/a	n/a
38	RAD21	chr4:7803824-7804224	HepG2	liver:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
39	RAD21	chr4:7803777-7804225	ECC-1	luminal epithelium:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
40	CTCF	chr4:7803813-7804248	K562	blood:	n/a	chr4:7804031-7804052 chr4:7804037-7804053 chr4:7804036-7804054
41	RAD21	chr4:7803808-7804259	H1-hESC	embryonic stem cell:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
42	CTCF	chr4:7803810-7804203	H1-hESC	embryonic stem cell:	n/a	chr4:7804031-7804052 chr4:7804037-7804053 chr4:7804036-7804054
43	CTCF	chr4:7803806-7804202	A549	lung:	n/a	chr4:7804031-7804052 chr4:7804037-7804053 chr4:7804036-7804054
44	CTCF	chr4:7803820-7803970	HVMF	connective:	n/a	n/a
45	CTCF	chr4:7803693-7804338	HCT-116	colon:	n/a	chr4:7804031-7804052 chr4:7804037-7804053 chr4:7804036-7804054
46	RAD21	chr4:7803786-7804154	GM12878	blood:	n/a	chr4:7804040-7804049 chr4:7804034-7804053
47	JUND	chr4:7803738-7804087	HepG2	liver:	n/a	chr4:7803890-7803899
48	ZNF384	chr4:7803543-7804170	GM12878	blood:	n/a	n/a
49	CTCF	chr4:7803821-7804300	HCT-116	colon:	n/a	chr4:7804031-7804052 chr4:7804037-7804053 chr4:7804036-7804054

No.	Distal block	Cell Line	Cell type
1	chr4:7803065..7804892-chr4:7807691..7809470,2	K562	blood:
2	chr4:7803065..7805141-chr4:7807691..7809396,2	K562	blood:
3	chr4:7770365..7771286-chr4:7803447..7804040,2	MCF-7	breast:
4	chr4:7763127..7763762-chr4:7803659..7804271,2	MCF-7	breast:
5	chr4:7763037..7763633-chr4:7803589..7804397,3	MCF-7	breast:
6	chr4:7771806..7772761-chr4:7803548..7804554,10	MCF-7	breast:

Variant related genes	Relation type
AFAP1	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10516188	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10937859	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1106248	0.89[ASN][1000 genomes]
rs11933020	0.90[ASN][1000 genomes]
rs12501415	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12505487	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12509628	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12511332	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12511919	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12512093	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12512166	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16841110	0.81[AMR][1000 genomes]
rs16841121	0.85[AMR][1000 genomes]
rs16841150	0.83[AMR][1000 genomes]
rs16841183	0.84[EUR][1000 genomes]
rs16841209	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16841268	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16841283	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16841288	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2269877	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2285763	0.80[AMR][1000 genomes]
rs34002186	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4074746	0.91[AFR][1000 genomes]
rs55851047	0.85[AFR][1000 genomes]
rs56264326	0.94[AFR][1000 genomes]
rs61166235	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6824231	0.84[EUR][1000 genomes]
rs730420	0.83[AMR][1000 genomes]
rs73797315	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs877707	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9683902	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9790478	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS 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	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1006642	chr4:7786980-7811291	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
2	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:7781600-7807400	Weak transcription	Brain Angular Gyrus	brain
5	chr4:7783800-7806200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
7	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr4:7789200-7806600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:7791000-7806600	Weak transcription	Psoas Muscle	Psoas
10	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr4:7791400-7806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:7796800-7804200	Strong transcription	NHEK	skin
13	chr4:7797000-7807000	Weak transcription	Liver	Liver
14	chr4:7798200-7807200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:7800200-7807200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:7800600-7805000	Weak transcription	Primary T cells from cord blood	blood
17	chr4:7800600-7806200	Weak transcription	Fetal Thymus	thymus
18	chr4:7800600-7828800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr4:7801000-7804000	Strong transcription	Osteobl	bone
20	chr4:7801400-7807200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr4:7801400-7807400	Weak transcription	Right Ventricle	heart
22	chr4:7801800-7807400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:7802000-7806200	Weak transcription	Fetal Brain Male	brain
24	chr4:7802000-7807200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:7802000-7807200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:7802000-7807800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:7802200-7805600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:7802200-7805600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:7802200-7806200	Weak transcription	Brain Substantia Nigra	brain
30	chr4:7802200-7819800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:7802400-7804800	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:7802400-7805600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:7802400-7806000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:7802400-7806200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr4:7802400-7806600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:7802400-7806800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:7802400-7812400	Weak transcription	Spleen	Spleen
38	chr4:7802600-7804600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr4:7802600-7806000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:7802600-7806000	Weak transcription	Adipose Nuclei	Adipose
41	chr4:7802600-7806200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:7802600-7806400	Weak transcription	Fetal Brain Female	brain
43	chr4:7802600-7806600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:7802600-7807200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr4:7802600-7807400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:7802600-7808000	Weak transcription	Gastric	stomach
47	chr4:7802600-7809600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:7802600-7810400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr4:7802800-7804800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:7802800-7804800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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