Variant report

Variant	rs714780
Chromosome Location	chr21:40178517-40178518
allele	G/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	MXI1	chr21:40176328-40180482	SK-N-SH	brain:	n/a	chr21:40176631-40176646 chr21:40176633-40176648
2	POLR2A	chr21:40175826-40184443	MCF10A-Er-Src	breast:	n/a	n/a
3	ZBTB7A	chr21:40177330-40178722	K562	blood:	n/a	chr21:40178114-40178125
4	POLR2A	chr21:40177100-40180919	PBDE	blood:	n/a	n/a
5	POLR2A	chr21:40176831-40178983	HL-60	blood:	n/a	n/a
6	EP300	chr21:40176364-40180305	SK-N-SH	brain:	n/a	chr21:40179345-40179359 chr21:40177988-40177997 chr21:40178219-40178228 chr21:40179343-40179357 chr21:40178259-40178275 chr21:40179344-40179358 chr21:40178028-40178044 chr21:40179342-40179356 chr21:40178328-40178344 chr21:40178322-40178331
7	CCNT2	chr21:40176993-40179135	K562	blood:	n/a	n/a
8	ZEB1	chr21:40178391-40178685	GM12878	blood:	n/a	n/a
9	CTCF	chr21:40178500-40178650	GM12875	blood:	n/a	n/a
10	POLR2A	chr21:40177260-40178541	NB4	blood:	n/a	n/a
11	POLR2A	chr21:40178423-40178722	ECC-1	luminal epithelium:	n/a	n/a
12	RAD21	chr21:40176426-40178698	MCF-7	breast:	n/a	chr21:40178543-40178556 chr21:40177096-40177109 chr21:40177093-40177112 chr21:40178101-40178114 chr21:40178124-40178136 chr21:40178030-40178044
13	POLR2A	chr21:40178128-40178769	Hela-S3	cervix:	n/a	n/a
14	TAL1	chr21:40177457-40179359	K562	blood:	n/a	n/a
15	MAX	chr21:40177192-40178616	GM12878	blood:	n/a	chr21:40177454-40177463 chr21:40178111-40178121 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
16	RAD21	chr21:40178129-40178554	H1-hESC	embryonic stem cell:	n/a	n/a
17	SMC3	chr21:40176607-40178615	Hela-S3	cervix:	n/a	chr21:40177519-40177533 chr21:40177325-40177332 chr21:40178167-40178177 chr21:40177094-40177108 chr21:40178332-40178342 chr21:40177523-40177533
18	ELF1	chr21:40177010-40178675	K562	blood:	n/a	chr21:40178512-40178524 chr21:40178154-40178163 chr21:40178051-40178063
19	HDAC2	chr21:40178274-40178599	K562	blood:	n/a	n/a
20	POLR2A	chr21:40177064-40178528	K562	blood:	n/a	n/a
21	SMC3	chr21:40175857-40180616	SK-N-SH	brain:	n/a	chr21:40177519-40177533 chr21:40177325-40177332 chr21:40178167-40178177 chr21:40177094-40177108 chr21:40178332-40178342 chr21:40177523-40177533
22	MAZ	chr21:40175795-40179353	IMR90	lung:	n/a	chr21:40176308-40176317 chr21:40176731-40176740 chr21:40177454-40177463 chr21:40176637-40176646 chr21:40176537-40176546 chr21:40178111-40178121 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
23	ELF1	chr21:40176917-40178751	GM12878	blood:	n/a	chr21:40178512-40178524 chr21:40178154-40178163 chr21:40178051-40178063
24	RAD21	chr21:40176569-40179264	IMR90	lung:	n/a	chr21:40178543-40178556 chr21:40177096-40177109 chr21:40177093-40177112 chr21:40178101-40178114 chr21:40178124-40178136 chr21:40178030-40178044
25	CTCF	chr21:40176319-40179110	SK-N-SH	brain:	n/a	chr21:40177982-40177995 chr21:40177095-40177108 chr21:40177092-40177110 chr21:40177520-40177533
26	ZBTB7A	chr21:40177295-40178867	ECC-1	luminal epithelium:	n/a	chr21:40178114-40178125
27	POLR2A	chr21:40175924-40187316	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr21:40178103-40178804	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr21:40176999-40178635	GM12892	blood:	n/a	n/a
30	CTBP2	chr21:40176884-40178663	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr21:40176867-40178704	MCF-7	breast:	n/a	n/a
32	HA-E2F1	chr21:40176753-40178798	MCF-7	breast:	n/a	chr21:40178507-40178517 chr21:40178473-40178483 chr21:40177209-40177226 chr21:40178322-40178331 chr21:40178104-40178114 chr21:40177212-40177223 chr21:40178219-40178228 chr21:40178529-40178540
33	CTCF	chr21:40178380-40178530	MCF-7	breast:	n/a	n/a
34	ELF1	chr21:40177300-40178676	K562	blood:	n/a	chr21:40178512-40178524 chr21:40178154-40178163 chr21:40178051-40178063
35	POLR2A	chr21:40178435-40178748	HUVEC	blood vessel:	n/a	n/a
36	E2F4	chr21:40178420-40178590	MCF10A-Er-Src	breast:	n/a	chr21:40178507-40178517 chr21:40178473-40178483 chr21:40178529-40178540
37	CTCF	chr21:40178400-40178550	HRE	kidney:	n/a	n/a
38	MAX	chr21:40176549-40178561	MCF-7	breast:	n/a	chr21:40176731-40176740 chr21:40177454-40177463 chr21:40176637-40176646 chr21:40178111-40178121 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
39	RCOR1	chr21:40178462-40178609	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr21:40176893-40178622	Hela-S3	cervix:	n/a	n/a
41	CHD2	chr21:40178487-40178569	K562	blood:	n/a	n/a
42	ZBTB7A	chr21:40177208-40178776	ECC-1	luminal epithelium:	n/a	chr21:40178114-40178125
43	HMGN3	chr21:40176914-40178751	K562	blood:	n/a	n/a
44	CHD1	chr21:40175807-40184420	IMR90	lung:	n/a	chr21:40183942-40183952
45	POLR2A	chr21:40176847-40178685	K562	blood:	n/a	n/a
46	MAX	chr21:40176544-40178784	K562	blood:	n/a	chr21:40176731-40176740 chr21:40177454-40177463 chr21:40176637-40176646 chr21:40178111-40178121 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
47	MAFK	chr21:40178444-40178532	Hela-S3	cervix:	n/a	n/a
48	BACH1	chr21:40178268-40178594	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr21:40177302-40178610	HepG2	liver:	n/a	n/a
50	GATA2	chr21:40178452-40180095	SH-SY5Y	brain:	n/a	chr21:40179944-40179951

No.	Distal block	Cell Line	Cell type
1	chr21:40175328..40180167-chr21:40553641..40558387,7	K562	blood:
2	chr21:40175328..40178574-chr21:40554098..40556223,3	K562	blood:
3	chr21:40176416..40179104-chr21:40257484..40260730,3	MCF-7	breast:
4	chr21:40113948..40115514-chr21:40177430..40179064,2	K562	blood:
5	chr21:40178030..40178651-chr9:140135018..140135878,2	Hela-S3	cervix:
6	chr21:40176601..40179515-chr21:40218059..40219886,2	K562	blood:
7	chr21:40174647..40179577-chr21:40285247..40287797,5	MCF-7	breast:
8	chr21:40178266..40180085-chr21:40683590..40685773,2	K562	blood:
9	chr21:40116993..40119222-chr21:40177945..40180622,2	MCF-7	breast:
10	chr21:40159708..40161955-chr21:40178038..40180627,4	K562	blood:
11	chr21:40177627..40180426-chr21:40542526..40544967,2	K562	blood:
12	chr21:40177965..40179709-chr21:40267730..40269357,2	K562	blood:
13	chr21:40176416..40178956-chr21:40498284..40502065,4	MCF-7	breast:
14	chr21:40084560..40086219-chr21:40178375..40180682,2	MCF-7	breast:
15	chr21:39459813..39461583-chr21:40177879..40180565,2	K562	blood:
16	chr21:40164421..40166863-chr21:40178031..40179684,2	MCF-7	breast:
17	chr21:40176263..40179138-chr21:40817088..40818717,2	K562	blood:

Variant related genes	Relation type
ETS2	TF binding region
ENSG00000272991	Chromatin interaction
ENSG00000234035	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000229925	Chromatin interaction
ENSG00000223806	Chromatin interaction
ENSG00000229986	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000228861	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000235701	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11701301	0.81[ASN][1000 genomes]
rs11911369	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17230954	0.85[ASN][1000 genomes]
rs17230961	0.85[ASN][1000 genomes]
rs2298560	0.89[ASN][1000 genomes]
rs2410062	0.85[ASN][1000 genomes]
rs2836715	0.81[ASN][1000 genomes]
rs2836717	0.81[ASN][1000 genomes]
rs2836720	0.81[ASN][1000 genomes]
rs2836724	0.81[ASN][1000 genomes]
rs28375993	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28508188	0.81[ASN][1000 genomes]
rs28817686	0.81[ASN][1000 genomes]
rs28836833	0.81[ASN][1000 genomes]
rs467698	0.81[ASN][1000 genomes]
rs467806	0.81[ASN][1000 genomes]
rs57740627	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59086904	0.81[ASN][1000 genomes]
rs60328145	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7278693	0.85[ASN][1000 genomes]
rs7279299	0.85[ASN][1000 genomes]
rs7283433	0.85[ASN][1000 genomes]
rs73450548	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73450552	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128181	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8133056	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8133164	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8134019	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8134441	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058591	chr21:40114130-40190594	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv3430408	chr21:40176482-40179580	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40176600-40179800	Active TSS	Rectal Smooth Muscle	rectum
2	chr21:40176600-40180400	Active TSS	Ovary	ovary
3	chr21:40176600-40181600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr21:40176600-40182000	Active TSS	Brain Anterior Caudate	brain
5	chr21:40176800-40179200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr21:40176800-40179200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr21:40176800-40179200	Active TSS	Stomach Mucosa	stomach
8	chr21:40176800-40179600	Active TSS	Psoas Muscle	Psoas
9	chr21:40176800-40179600	Active TSS	A549	lung
10	chr21:40176800-40179800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr21:40176800-40179800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr21:40176800-40180000	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr21:40176800-40180000	Active TSS	Aorta	Aorta
14	chr21:40176800-40180000	Active TSS	Fetal Kidney	kidney
15	chr21:40176800-40180000	Active TSS	Thymus	Thymus
16	chr21:40176800-40180400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr21:40176800-40180600	Active TSS	Brain Substantia Nigra	brain
18	chr21:40176800-40181000	Active TSS	Brain Angular Gyrus	brain
19	chr21:40176800-40182800	Active TSS	Brain Cingulate Gyrus	brain
20	chr21:40176800-40182800	Active TSS	Brain Hippocampus Middle	brain
21	chr21:40177000-40178600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr21:40177000-40178600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr21:40177000-40178800	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr21:40177000-40178800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr21:40177000-40178800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
26	chr21:40177000-40178800	Active TSS	HSMM	muscle
27	chr21:40177000-40179000	Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr21:40177000-40179000	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr21:40177000-40179200	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr21:40177000-40179200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr21:40177000-40179200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr21:40177000-40179400	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr21:40177000-40179600	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr21:40177000-40179600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr21:40177000-40179600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr21:40177000-40179600	Active TSS	Colon Smooth Muscle	Colon
37	chr21:40177000-40179800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr21:40177000-40179800	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr21:40177000-40179800	Active TSS	Liver	Liver
40	chr21:40177000-40179800	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr21:40177000-40180000	Active TSS	Esophagus	oesophagus
42	chr21:40177000-40180600	Active TSS	Gastric	stomach
43	chr21:40177000-40180600	Active TSS	Small Intestine	intestine
44	chr21:40177000-40181400	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr21:40177200-40178600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr21:40177200-40178800	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr21:40177200-40179200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr21:40177200-40179400	Active TSS	H1 Cell Line	embryonic stem cell
49	chr21:40177200-40179400	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr21:40177200-40179600	Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links