Variant report

Variant	rs7564789
Chromosome Location	chr2:11272957-11272958
allele	C/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	TAF1	chr2:11272869-11273474	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr2:11272820-11272970	HAc	cerebellar:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
3	CTCF	chr2:11272703-11273086	SK-N-SH_RA	brain:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
4	RAD21	chr2:11272585-11273337	HepG2	liver:	n/a	chr2:11272908-11272921 chr2:11272905-11272924
5	GABPA	chr2:11272628-11273328	A549	lung:	n/a	n/a
6	NR3C1	chr2:11272714-11273622	A549	lung:	n/a	chr2:11273361-11273375 chr2:11273360-11273376 chr2:11273361-11273375 chr2:11273360-11273376 chr2:11273357-11273378 chr2:11273090-11273104 chr2:11273360-11273376 chr2:11273360-11273376 chr2:11273355-11273381 chr2:11273358-11273371
7	TCF12	chr2:11272715-11273346	A549	lung:	n/a	n/a
8	REST	chr2:11272590-11273463	A549	lung:	n/a	chr2:11273188-11273197
9	CEBPB	chr2:11272777-11273302	IMR90	lung:	n/a	n/a
10	ELF1	chr2:11272608-11273291	K562	blood:	n/a	n/a
11	SMC3	chr2:11272685-11273402	HepG2	liver:	n/a	chr2:11272906-11272920
12	WRNIP1	chr2:11272822-11273032	GM12878	blood:	n/a	n/a
13	MAZ	chr2:11272719-11273271	Hela-S3	cervix:	n/a	n/a
14	RCOR1	chr2:11272629-11273221	K562	blood:	n/a	n/a
15	MXI1	chr2:11272794-11273402	Hela-S3	cervix:	n/a	chr2:11273196-11273211
16	SMC3	chr2:11272698-11273286	GM12878	blood:	n/a	chr2:11272906-11272920
17	MAX	chr2:11272471-11273510	MCF-7	breast:	n/a	n/a
18	BRCA1	chr2:11272815-11272974	HepG2	liver:	n/a	n/a
19	ELK1	chr2:11272764-11273207	GM12878	blood:	n/a	n/a
20	CTCF	chr2:11272712-11273102	ECC-1	luminal epithelium:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
21	RAD21	chr2:11272690-11273135	Hela-S3	cervix:	n/a	chr2:11272908-11272921 chr2:11272905-11272924
22	GTF2F1	chr2:11272685-11273086	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr2:11272820-11272970	GM12865	blood:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
24	CTCF	chr2:11272743-11273039	MCF-7	breast:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
25	SP4	chr2:11272686-11273354	H1-hESC	embryonic stem cell:	n/a	chr2:11273008-11273024 chr2:11273067-11273083 chr2:11273170-11273186 chr2:11273014-11273025
26	CTCF	chr2:11272820-11272970	GM12875	blood:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
27	CTCF	chr2:11272654-11273103	H1-hESC	embryonic stem cell:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
28	CTCF	chr2:11272840-11272990	HPAF	blood vessel:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
29	REST	chr2:11272683-11273399	PFSK-1	brain:	n/a	chr2:11273188-11273197
30	CTCF	chr2:11272840-11272990	WERI-Rb-1	eye:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
31	RCOR1	chr2:11272664-11273198	Hela-S3	cervix:	n/a	n/a
32	TBP	chr2:11272689-11273439	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr2:11272764-11273045	Medullo	brain:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
34	CTCF	chr2:11272840-11272990	GM06990	blood:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
35	MYC	chr2:11272781-11273265	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr2:11272659-11273257	A549	lung:	n/a	n/a
37	EBF1	chr2:11272685-11273055	GM12878	blood:	n/a	n/a
38	SIN3AK20	chr2:11272763-11273399	HepG2	liver:	n/a	n/a
39	CTCF	chr2:11272749-11273045	GM10248	blood:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
40	CTCF	chr2:11272860-11273010	GM12866	blood:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
41	CTCF	chr2:11272840-11272990	RPTEC	kidney:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
42	ZNF143	chr2:11272716-11273165	GM12878	blood:	n/a	n/a
43	CTCF	chr2:11272840-11272990	HEK293	kidney:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
44	CTCF	chr2:11272677-11273113	H1-hESC	embryonic stem cell:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
45	MXI1	chr2:11272770-11273358	H1-hESC	embryonic stem cell:	n/a	chr2:11273196-11273211
46	MAX	chr2:11272720-11273296	A549	lung:	n/a	n/a
47	YY1	chr2:11272744-11273088	K562	blood:	n/a	n/a
48	CTCF	chr2:11272780-11273032	T-47D	breast:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
49	CTCF	chr2:11272840-11272990	SAEC	small airway:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
50	CTCF	chr2:11272840-11272990	Hela-S3	cervix:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927

No.	Distal block	Cell Line	Cell type
1	chr2:11272046..11273363-chr2:11723821..11725006,6	K562	blood:
2	chr2:11272147..11274930-chr2:11671339..11675156,3	MCF-7	breast:
3	chr2:11271098..11275692-chr2:11293512..11297101,4	MCF-7	breast:
4	chr2:10828291..10832221-chr2:11269738..11273006,3	MCF-7	breast:
5	chr2:11269728..11273923-chr2:11678087..11684060,5	MCF-7	breast:
6	chr2:10972589..10973103-chr2:11272836..11273401,2	MCF-7	breast:

Variant related genes	Relation type
C2orf50	TF binding region
ENSG00000145063	TF binding region
ENSG00000239899	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000143870	Chromatin interaction
ENSG00000115761	Chromatin interaction
ENSG00000243819	Chromatin interaction
ENSG00000162976	Chromatin interaction
ENSG00000264010	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11903207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810295	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2102714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4297854	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4386295	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4446053	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4474856	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4474857	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4476323	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4635508	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56732337	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57447764	0.92[EUR][1000 genomes]
rs57604212	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57812764	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432175	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432176	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6432179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432180	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6706759	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708309	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713752	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713861	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717010	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726867	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736273	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753482	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760152	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175630	0.84[EUR][1000 genomes]
rs73175632	0.84[EUR][1000 genomes]
rs73175633	0.84[EUR][1000 genomes]
rs73189609	1.00[EUR][1000 genomes]
rs7563857	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7573202	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579736	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7600174	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7600586	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs908276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520789	chr2:11259067-11312224	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11269800-11274000	Enhancers	Fetal Brain Male	brain
2	chr2:11270400-11273000	Weak transcription	Aorta	Aorta
3	chr2:11270400-11273000	Weak transcription	Esophagus	oesophagus
4	chr2:11270600-11273000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:11270600-11273000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:11270600-11273000	Weak transcription	Lung	lung
7	chr2:11270600-11273200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr2:11270800-11273000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:11270800-11273000	Weak transcription	Fetal Heart	heart
10	chr2:11271000-11273000	Weak transcription	Small Intestine	intestine
11	chr2:11271400-11273200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:11271400-11274200	Active TSS	Brain Anterior Caudate	brain
13	chr2:11271800-11273200	Active TSS	Brain Hippocampus Middle	brain
14	chr2:11271800-11273600	Active TSS	Brain Cingulate Gyrus	brain
15	chr2:11272200-11273200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:11272400-11273000	Enhancers	NHLF	lung
17	chr2:11272400-11273400	Enhancers	Spleen	Spleen
18	chr2:11272400-11273600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr2:11272400-11273600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr2:11272400-11273600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:11272400-11274000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:11272600-11273000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr2:11272600-11273000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:11272600-11273000	Enhancers	Gastric	stomach
25	chr2:11272600-11273000	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr2:11272600-11273000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
27	chr2:11272600-11273000	Enhancers	NHDF-Ad	bronchial
28	chr2:11272600-11273200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:11272600-11273400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr2:11272600-11273400	Active TSS	Fetal Brain Female	brain
31	chr2:11272600-11273400	Flanking Active TSS	Fetal Thymus	thymus
32	chr2:11272600-11273400	Flanking Active TSS	Dnd41	blood
33	chr2:11272600-11273600	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr2:11272600-11273600	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr2:11272600-11273600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr2:11272600-11273600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr2:11272600-11273600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr2:11272600-11273600	Flanking Active TSS	Hela-S3	cervix
39	chr2:11272600-11273800	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr2:11272600-11273800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:11272600-11273800	Flanking Active TSS	Colonic Mucosa	Colon
42	chr2:11272800-11273000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr2:11272800-11273000	Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr2:11272800-11273000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr2:11272800-11273000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:11272800-11273000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:11272800-11273000	Active TSS	Duodenum Mucosa	Duodenum
48	chr2:11272800-11273000	Flanking Active TSS	Fetal Stomach	stomach
49	chr2:11272800-11273000	Enhancers	HMEC	breast
50	chr2:11272800-11273200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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