Variant report

Variant	rs6739757
Chromosome Location	chr2:234292964-234292965
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	CTCF	chr2:234292880-234293030	SAEC	small airway:	n/a	n/a
2	CTCF	chr2:234292820-234292970	HCPEpiC	choroid plexus:	n/a	chr2:234292857-234292866
3	RUNX3	chr2:234292640-234293041	GM12878	blood:	n/a	n/a
4	RCOR1	chr2:234292694-234293038	K562	blood:	n/a	n/a
5	MAZ	chr2:234292693-234293049	K562	blood:	n/a	n/a
6	CTCF	chr2:234292661-234293057	K562	blood:	n/a	chr2:234292857-234292866
7	CTCF	chr2:234292840-234292990	K562	blood:	n/a	chr2:234292857-234292866
8	CTCF	chr2:234292820-234292970	HPF	lung:	n/a	chr2:234292857-234292866
9	RAD21	chr2:234292683-234292991	HepG2	liver:	n/a	chr2:234292857-234292870
10	YY1	chr2:234292685-234293005	GM12892	blood:	n/a	n/a
11	CTCF	chr2:234292768-234292975	GM19238	blood:	n/a	chr2:234292857-234292866
12	CTCF	chr2:234292820-234292970	HEK293	kidney:	n/a	chr2:234292857-234292866
13	CTCF	chr2:234292675-234293070	K562	blood:	n/a	chr2:234292857-234292866
14	CTCF	chr2:234292820-234292970	SK-N-SH_RA	brain:	n/a	chr2:234292857-234292866
15	SMC3	chr2:234292704-234292994	K562	blood:	n/a	chr2:234292860-234292867
16	CTCF	chr2:234292840-234292990	MCF-7	breast:	n/a	chr2:234292857-234292866
17	TBL1XR1	chr2:234292849-234292987	GM12878	blood:	n/a	n/a
18	CTCF	chr2:234292747-234292987	GM12892	blood:	n/a	chr2:234292857-234292866
19	RAD21	chr2:234292625-234293041	HepG2	liver:	n/a	chr2:234292857-234292870
20	CTCF	chr2:234292820-234292970	GM12864	blood:	n/a	chr2:234292857-234292866
21	CTCF	chr2:234292840-234292990	HRPEpiC	eye:	n/a	chr2:234292857-234292866
22	NR2F2	chr2:234292587-234293063	K562	blood:	n/a	n/a
23	RAD21	chr2:234292814-234292977	A549	lung:	n/a	chr2:234292857-234292870
24	CTCF	chr2:234292763-234292971	MCF-7	breast:	n/a	chr2:234292857-234292866
25	CTCF	chr2:234292820-234292970	GM12869	blood:	n/a	chr2:234292857-234292866
26	ZNF384	chr2:234292672-234293009	K562	blood:	n/a	n/a
27	CTCF	chr2:234292820-234292970	A549	lung:	n/a	chr2:234292857-234292866
28	RAD21	chr2:234292719-234292968	HepG2	liver:	n/a	chr2:234292857-234292870
29	BHLHE40	chr2:234292685-234293003	K562	blood:	n/a	n/a
30	CTCF	chr2:234292820-234292970	GM12874	blood:	n/a	chr2:234292857-234292866
31	CTCF	chr2:234292840-234292990	GM12872	blood:	n/a	chr2:234292857-234292866
32	SMC3	chr2:234292774-234292974	HepG2	liver:	n/a	chr2:234292860-234292867
33	RAD21	chr2:234292693-234292984	GM12878	blood:	n/a	chr2:234292857-234292870
34	MAFK	chr2:234292498-234293330	HepG2	liver:	n/a	chr2:234292970-234292985 chr2:234292635-234292650 chr2:234293174-234293188 chr2:234293180-234293191 chr2:234293176-234293191 chr2:234293176-234293192 chr2:234293173-234293189 chr2:234293171-234293191
35	CTCF	chr2:234292840-234292990	GM12870	blood:	n/a	chr2:234292857-234292866
36	CTCF	chr2:234292732-234292982	GM12878	blood:	n/a	chr2:234292857-234292866
37	CTCF	chr2:234292745-234292988	K562	blood:	n/a	chr2:234292857-234292866
38	RAD21	chr2:234292674-234292985	K562	blood:	n/a	chr2:234292857-234292870
39	CTCF	chr2:234292820-234292970	GM12872	blood:	n/a	chr2:234292857-234292866
40	RAD21	chr2:234292710-234293002	H1-hESC	embryonic stem cell:	n/a	chr2:234292857-234292870
41	GATA3	chr2:234292588-234293001	MCF-7	breast:	n/a	chr2:234292814-234292823
42	CTCF	chr2:234292840-234292990	A549	lung:	n/a	chr2:234292857-234292866
43	CTCF	chr2:234292820-234292970	HBMEC	blood vessel:	n/a	chr2:234292857-234292866
44	CTCF	chr2:234292840-234292990	SK-N-SH_RA	brain:	n/a	chr2:234292857-234292866
45	JUND	chr2:234292731-234293014	K562	blood:	n/a	n/a
46	CTCF	chr2:234292718-234292984	HepG2	liver:	n/a	chr2:234292857-234292866
47	CTCF	chr2:234292840-234292990	HCPEpiC	choroid plexus:	n/a	chr2:234292857-234292866
48	CTCF	chr2:234292591-234293201	A549	lung:	n/a	chr2:234292857-234292866
49	CTCF	chr2:234292676-234293029	K562	blood:	n/a	chr2:234292857-234292866

No.	Distal block	Cell Line	Cell type
1	chr2:234259434..234265610-chr2:234290886..234296562,9	MCF-7	breast:
2	chr2:234292070..234294223-chr2:234599510..234601905,2	MCF-7	breast:
3	chr2:234289741..234291350-chr2:234292115..234294515,2	K562	blood:

Variant related genes	Relation type
DGKD	TF binding region
ENSG00000201013	TF binding region
ENSG00000243637	Chromatin interaction
ENSG00000077044	Chromatin interaction
ENSG00000259793	Chromatin interaction
ENSG00000167165	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10153744	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11679773	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13413505	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28373304	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55983182	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58373601	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6431364	0.93[EUR][1000 genomes]
rs6722763	0.93[EUR][1000 genomes]
rs6759246	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7566221	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7576633	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7580412	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234264600-234307600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:234265000-234295000	Weak transcription	Osteobl	bone
3	chr2:234265200-234295000	Weak transcription	NH-A	brain
4	chr2:234265800-234293000	Weak transcription	HMEC	breast
5	chr2:234266000-234293000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:234266400-234294000	Weak transcription	Fetal Brain Male	brain
7	chr2:234268400-234293400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:234269200-234293400	Weak transcription	Right Atrium	heart
9	chr2:234270000-234322400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:234272800-234313200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:234274000-234295200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:234277600-234322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:234278600-234293000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:234278600-234293600	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:234278600-234293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:234278600-234294000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:234278600-234294000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:234278800-234293000	Weak transcription	Brain Substantia Nigra	brain
19	chr2:234279000-234293000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:234279200-234293200	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:234279200-234293400	Weak transcription	Brain Anterior Caudate	brain
22	chr2:234279200-234293600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:234279200-234294400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:234280400-234294800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:234280600-234293200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:234281800-234296600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:234282200-234293000	Weak transcription	Gastric	stomach
28	chr2:234282200-234293400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:234282200-234293600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:234282400-234294400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:234282400-234298000	Weak transcription	Dnd41	blood
32	chr2:234284000-234293800	Weak transcription	Colonic Mucosa	Colon
33	chr2:234284800-234295400	Weak transcription	Fetal Intestine Large	intestine
34	chr2:234285000-234295400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:234287400-234294800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr2:234289000-234293000	Weak transcription	Brain Germinal Matrix	brain
37	chr2:234289000-234307600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:234289200-234293000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:234289400-234293200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:234289400-234293400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:234289400-234293400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:234289600-234294600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr2:234289800-234293200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:234290000-234293400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:234290000-234293600	Weak transcription	Spleen	Spleen
46	chr2:234290200-234293000	Weak transcription	Stomach Mucosa	stomach
47	chr2:234290200-234293200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:234290200-234294800	Weak transcription	Small Intestine	intestine
49	chr2:234290400-234293000	Weak transcription	Liver	Liver
50	chr2:234290400-234293400	Weak transcription	Adipose Nuclei	Adipose

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