Variant report

Variant	rs2276834
Chromosome Location	chr3:52325759-52325760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:99)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:99 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr3:52324976-52326193	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr3:52325431-52325886	K562	blood:	n/a	n/a
3	CTCF	chr3:52325542-52325768	Medullo	brain:	n/a	n/a
4	FOXM1	chr3:52325346-52325933	GM12878	blood:	n/a	n/a
5	CTCF	chr3:52325520-52325774	Gliobla	brain:	n/a	n/a
6	CTCF	chr3:52325403-52325880	GM12878	blood:	n/a	n/a
7	CTCF	chr3:52325640-52325790	HAc	cerebellar:	n/a	n/a
8	CTCF	chr3:52325476-52325802	Spleen_OC	spleen:	n/a	n/a
9	RUNX3	chr3:52325419-52325876	GM12878	blood:	n/a	n/a
10	MYBL2	chr3:52325267-52325918	HepG2	liver:	n/a	n/a
11	RAD21	chr3:52325449-52326008	GM12878	blood:	n/a	n/a
12	RAD21	chr3:52325413-52326021	ECC-1	luminal epithelium:	n/a	n/a
13	RAD21	chr3:52325366-52325922	MCF-7	breast:	n/a	n/a
14	MTA3	chr3:52325203-52325820	GM12878	blood:	n/a	n/a
15	CTCF	chr3:52325465-52325776	SK-N-SH_RA	brain:	n/a	n/a
16	IRF3	chr3:52325681-52325808	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:52323413-52325803	HepG2	liver:	n/a	n/a
18	ZNF143	chr3:52325574-52325774	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr3:52325262-52325998	A549	lung:	n/a	n/a
20	RAD21	chr3:52325478-52325841	K562	blood:	n/a	n/a
21	POLR2A	chr3:52325404-52325891	H1-neurons	neurons:	n/a	n/a
22	CTCF	chr3:52325441-52325876	HepG2	liver:	n/a	n/a
23	RAD21	chr3:52325378-52326038	HCT-116	colon:	n/a	n/a
24	RAD21	chr3:52325463-52325880	GM12878	blood:	n/a	n/a
25	CTCF	chr3:52325473-52325832	GM12892	blood:	n/a	n/a
26	SMC3	chr3:52325397-52325853	HepG2	liver:	n/a	n/a
27	RAD21	chr3:52325433-52325868	HepG2	liver:	n/a	n/a
28	CTCF	chr3:52325501-52325788	Hela-S3	cervix:	n/a	n/a
29	RAD21	chr3:52325398-52326044	A549	lung:	n/a	n/a
30	CTCF	chr3:52325414-52325836	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr3:52325502-52325785	MCF-7	breast:	n/a	n/a
32	CTCF	chr3:52325508-52325767	K562	blood:	n/a	n/a
33	CTCF	chr3:52325478-52325796	HepG2	liver:	n/a	n/a
34	CTCF	chr3:52325467-52325794	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr3:52325479-52325824	GM19239	blood:	n/a	n/a
36	CTCF	chr3:52325520-52325790	GM12868	blood:	n/a	n/a
37	ZBTB7A	chr3:52325561-52325782	HepG2	liver:	n/a	n/a
38	RAD21	chr3:52325426-52325841	Hela-S3	cervix:	n/a	n/a
39	WRNIP1	chr3:52325588-52325785	GM12878	blood:	n/a	n/a
40	CTCF	chr3:52325453-52325835	GM19238	blood:	n/a	n/a
41	CTCF	chr3:52325524-52325773	HUVEC	blood vessel:	n/a	n/a
42	CTCF	chr3:52325500-52325829	K562	blood:	n/a	n/a
43	YY1	chr3:52325458-52325794	GM12878	blood:	n/a	n/a
44	SMC3	chr3:52325419-52325895	K562	blood:	n/a	n/a
45	CTCF	chr3:52325366-52325908	MCF-7	breast:	n/a	n/a
46	SMC3	chr3:52325459-52325845	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr3:52325472-52325801	GM12878	blood:	n/a	n/a
48	ZNF143	chr3:52325467-52325814	GM12878	blood:	n/a	n/a
49	RAD21	chr3:52325360-52325870	H1-hESC	embryonic stem cell:	n/a	n/a
50	RAD21	chr3:52325503-52325854	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52318594..52322784-chr3:52322985..52327026,4	MCF-7	breast:
2	chr3:52325192..52326082-chr3:52419115..52419793,5	MCF-7	breast:
3	chr3:52325177..52326410-chr3:52373105..52374205,12	K562	blood:
4	chr3:52309930..52312660-chr3:52325068..52328067,2	K562	blood:
5	chr3:52321086..52323733-chr3:52324166..52327461,5	MCF-7	breast:
6	chr3:52325194..52326110-chr3:52418963..52419968,4	K562	blood:
7	chr3:52325390..52326371-chr3:52418909..52419771,3	MCF-7	breast:
8	chr3:52324588..52327004-chr3:52442941..52444727,2	MCF-7	breast:
9	chr3:52325201..52326075-chr3:52373199..52374128,6	MCF-7	breast:
10	chr3:52325231..52326092-chr3:52373318..52374482,3	MCF-7	breast:

No data

Variant related genes	Relation type
WDR82	TF binding region
ENSG00000164091	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000163930	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1060330	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11705963	0.84[AFR][1000 genomes]
rs11706108	0.84[AFR][1000 genomes]
rs11717383	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13091545	0.84[AFR][1000 genomes]
rs34228726	0.85[ASN][1000 genomes]
rs34569561	0.83[ASN][1000 genomes]
rs353547	0.86[ASN][1000 genomes]
rs35860312	0.82[AFR][1000 genomes]
rs3844291	0.85[ASN][1000 genomes]
rs3852063	0.88[ASN][1000 genomes]
rs3852064	0.87[ASN][1000 genomes]
rs57615517	0.84[ASN][1000 genomes]
rs57630131	0.80[ASN][1000 genomes]
rs59565798	0.85[ASN][1000 genomes]
rs610060	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6445358	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66462821	0.82[AFR][1000 genomes]
rs6794675	0.84[AFR][1000 genomes]
rs730050	0.95[ASN][1000 genomes]
rs7614727	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618915	0.83[ASN][1000 genomes]
rs7622851	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7629072	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7643570	0.84[AFR][1000 genomes]
rs9311474	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
5	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
7	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
8	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
9	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
10	esv3402579	chr3:52323712-52330410	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2276834	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs2276834	GLYCTK	cis	Whole Blood	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52322600-52331800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52322600-52332000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:52322600-52334400	Weak transcription	NHDF-Ad	bronchial
4	chr3:52322800-52325800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:52322800-52326400	Weak transcription	Fetal Brain Female	brain
6	chr3:52322800-52330800	Weak transcription	Brain Germinal Matrix	brain
7	chr3:52322800-52331400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:52322800-52331400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:52322800-52331600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:52322800-52331800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:52323000-52325800	Weak transcription	NHEK	skin
12	chr3:52323000-52326000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:52323000-52326000	Weak transcription	Aorta	Aorta
14	chr3:52323000-52328200	Weak transcription	Psoas Muscle	Psoas
15	chr3:52323000-52332600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:52323200-52341000	Weak transcription	Small Intestine	intestine
17	chr3:52323400-52326200	Weak transcription	HSMMtube	muscle
18	chr3:52323400-52333200	Weak transcription	HUVEC	blood vessel
19	chr3:52323600-52326800	Weak transcription	Hela-S3	cervix
20	chr3:52323600-52328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:52323600-52330400	Weak transcription	HSMM	muscle
22	chr3:52323800-52329800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:52324000-52331800	Weak transcription	K562	blood
24	chr3:52324000-52332800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:52324200-52326200	Strong transcription	Lung	lung
26	chr3:52324200-52328200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:52324200-52331400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:52324400-52328800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:52324400-52328800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:52324400-52329600	Strong transcription	Thymus	Thymus
31	chr3:52324400-52330200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:52324400-52331000	Strong transcription	Primary T cells from cord blood	blood
33	chr3:52324400-52332000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:52324600-52325800	Flanking Active TSS	Stomach Mucosa	stomach
35	chr3:52324600-52326000	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
36	chr3:52324600-52326600	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr3:52324600-52326800	Genic enhancers	Gastric	stomach
38	chr3:52324600-52327800	Strong transcription	Esophagus	oesophagus
39	chr3:52324600-52328200	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr3:52324600-52329000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:52324600-52329200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:52324600-52329400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:52324600-52329600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr3:52324600-52329600	Strong transcription	Fetal Muscle Leg	muscle
45	chr3:52324600-52330200	Strong transcription	Placenta	Placenta
46	chr3:52324600-52330400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:52324600-52330600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr3:52324800-52325800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr3:52324800-52326200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr3:52324800-52326200	Flanking Active TSS	Liver	Liver

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