Variant report

Variant	rs56217714
Chromosome Location	chr2:38827965-38827966
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr2:38827530-38827988	HepG2	liver:	n/a	n/a
2	UBTF	chr2:38827449-38828326	K562	blood:	n/a	n/a
3	POLR2A	chr2:38825324-38828171	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:38827477-38828045	HepG2	liver:	n/a	n/a
5	RCOR1	chr2:38827616-38827990	K562	blood:	n/a	n/a
6	TBL1XR1	chr2:38826587-38828368	K562	blood:	n/a	n/a
7	RAD21	chr2:38827547-38831481	SK-N-SH	brain:	n/a	n/a
8	TEAD4	chr2:38826023-38827980	HepG2	liver:	n/a	n/a
9	MAX	chr2:38827655-38827995	K562	blood:	n/a	n/a
10	POLR2A	chr2:38827909-38828025	MCF-7	breast:	n/a	n/a
11	ARID3A	chr2:38827668-38828272	K562	blood:	n/a	n/a
12	CUX1	chr2:38827833-38828355	K562	blood:	n/a	n/a
13	POLR2A	chr2:38827448-38828045	HL-60	blood:	n/a	n/a
14	POLR2A	chr2:38827812-38828017	MCF10A-Er-Src	breast:	n/a	n/a
15	MAZ	chr2:38827667-38828017	K562	blood:	n/a	n/a
16	TBP	chr2:38827603-38827994	K562	blood:	n/a	n/a
17	TEAD4	chr2:38826847-38828457	K562	blood:	n/a	n/a
18	TAF1	chr2:38827760-38828021	K562	blood:	n/a	n/a
19	CHD1	chr2:38827485-38831648	IMR90	lung:	n/a	n/a
20	SMC3	chr2:38827460-38831532	SK-N-SH	brain:	n/a	chr2:38830755-38830765 chr2:38830289-38830299
21	SIN3AK20	chr2:38827610-38827967	SK-N-SH	brain:	n/a	n/a
22	GATA2	chr2:38827654-38827975	SH-SY5Y	brain:	n/a	n/a
23	TRIM28	chr2:38827392-38828272	K562	blood:	n/a	n/a
24	POLR2A	chr2:38821640-38832164	K562	blood:	n/a	n/a
25	MYBL2	chr2:38826556-38828048	HepG2	liver:	n/a	n/a
26	MBD4	chr2:38826651-38828360	HepG2	liver:	n/a	n/a
27	ZNF384	chr2:38827562-38828538	K562	blood:	n/a	chr2:38828250-38828258
28	HCFC1	chr2:38827862-38827996	K562	blood:	n/a	n/a
29	MYC	chr2:38827962-38827982	MCF10A-Er-Src	breast:	n/a	n/a
30	IRF1	chr2:38827592-38829041	K562	blood:	n/a	chr2:38828237-38828244
31	POLR2A	chr2:38827686-38827966	K562	blood:	n/a	n/a
32	UBTF	chr2:38827334-38831119	K562	blood:	n/a	n/a
33	ZNF263	chr2:38827465-38828002	HEK293-T-REx	kidney:	n/a	n/a
34	BHLHE40	chr2:38827738-38827974	K562	blood:	n/a	n/a
35	MYC	chr2:38827731-38828156	K562	blood:	n/a	n/a
36	SIN3A	chr2:38827826-38827995	H1-hESC	embryonic stem cell:	n/a	n/a
37	HEY1	chr2:38827361-38828038	HepG2	liver:	n/a	n/a
38	POLR2A	chr2:38827474-38827966	K562	blood:	n/a	n/a
39	POLR2A	chr2:38825282-38829280	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38827534..38829774-chr2:38906960..38909388,3	K562	blood:
2	chr2:38825670..38832919-chr2:38891527..38903424,21	K562	blood:
3	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
4	chr2:38824811..38832919-chr2:38891494..38898299,16	K562	blood:
5	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
6	chr2:38816751..38822030-chr2:38827238..38830922,5	MCF-7	breast:
7	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
8	chr2:38821957..38830238-chr2:38965333..38974515,17	K562	blood:
9	chr2:38816590..38821819-chr2:38825503..38830021,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235586	TF binding region
HNRNPLL	TF binding region
ENSG00000143889	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000232518	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10495880	0.82[ASN][1000 genomes]
rs12105827	0.88[EUR][1000 genomes]
rs12987111	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12990659	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12995222	0.87[ASN][1000 genomes]
rs12996029	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13011896	0.96[AFR][1000 genomes]
rs1540436	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17421399	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17421503	0.83[AFR][1000 genomes]
rs17421743	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17493321	0.88[EUR][1000 genomes]
rs17493419	0.83[AFR][1000 genomes]
rs17493538	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17493573	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17493594	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1864828	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1864829	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1864830	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3213851	0.94[ASN][1000 genomes]
rs34218951	0.87[EUR][1000 genomes]
rs34462852	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35679136	0.88[AFR][1000 genomes]
rs35734673	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35933789	0.97[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4268910	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6544170	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6721860	0.80[EUR][1000 genomes]
rs6745023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757844	0.84[EUR][1000 genomes]
rs68109027	0.81[AFR][1000 genomes]
rs72905846	0.81[AFR][1000 genomes]
rs72905865	0.82[ASN][1000 genomes]
rs72907903	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7573095	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7574556	0.88[EUR][1000 genomes]
rs934394	0.83[AFR][1000 genomes]
rs934395	0.83[AFR][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38822400-38828600	Weak transcription	Lung	lung
2	chr2:38822800-38830400	Active TSS	Primary T cells fromperipheralblood	blood
3	chr2:38824400-38828200	Enhancers	Fetal Heart	heart
4	chr2:38825000-38830600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:38825200-38828400	Enhancers	Liver	Liver
6	chr2:38825200-38831000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:38825400-38828000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:38825400-38828000	Enhancers	Primary T cells from cord blood	blood
9	chr2:38825400-38828400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr2:38825600-38830800	Active TSS	Stomach Smooth Muscle	stomach
11	chr2:38825800-38828200	Flanking Active TSS	A549	lung
12	chr2:38825800-38828800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:38826200-38828200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:38826200-38828200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:38826200-38830800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:38826400-38830600	Active TSS	K562	blood
17	chr2:38826400-38831400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:38826600-38828400	Weak transcription	Stomach Mucosa	stomach
19	chr2:38826800-38828000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr2:38826800-38828000	Flanking Active TSS	Osteobl	bone
21	chr2:38826800-38828400	Flanking Active TSS	HUVEC	blood vessel
22	chr2:38826800-38830600	Active TSS	NHLF	lung
23	chr2:38826800-38831000	Active TSS	Duodenum Mucosa	Duodenum
24	chr2:38827000-38828000	Enhancers	Primary hematopoietic stem cells	blood
25	chr2:38827000-38828000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:38827000-38828000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr2:38827000-38828000	Flanking Active TSS	NHEK	skin
28	chr2:38827000-38828600	Active TSS	Brain Cingulate Gyrus	brain
29	chr2:38827000-38830600	Active TSS	Aorta	Aorta
30	chr2:38827000-38830800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:38827000-38830800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:38827000-38830800	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr2:38827000-38830800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:38827000-38831400	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr2:38827200-38828000	Flanking Active TSS	Fetal Brain Male	brain
36	chr2:38827200-38828400	Weak transcription	Brain Substantia Nigra	brain
37	chr2:38827200-38828400	Flanking Active TSS	Dnd41	blood
38	chr2:38827200-38830400	Active TSS	HMEC	breast
39	chr2:38827200-38830600	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr2:38827200-38830600	Active TSS	NH-A	brain
41	chr2:38827200-38830800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:38827200-38830800	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr2:38827200-38830800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:38827200-38830800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:38827200-38830800	Active TSS	Fetal Intestine Small	intestine
46	chr2:38827200-38831000	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr2:38827200-38831000	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr2:38827200-38831000	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr2:38827200-38831200	Active TSS	Brain Germinal Matrix	brain
50	chr2:38827400-38828000	Flanking Active TSS	H1 Cell Line	embryonic stem cell

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