Variant report

Variant	rs9977041
Chromosome Location	chr21:46495399-46495400
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:66)
CpG islands
(count:61)
Chromatin interactive
region (count:49)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:66 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr21:46494944-46495569	Hela-S3	cervix:	n/a	n/a
2	EBF1	chr21:46494920-46495443	GM12878	blood:	n/a	chr21:46495207-46495218 chr21:46495208-46495217 chr21:46495206-46495219 chr21:46495208-46495217 chr21:46495208-46495218
3	MAX	chr21:46493074-46495782	MCF-7	breast:	n/a	n/a
4	POLR2A	chr21:46493084-46495667	K562	blood:	n/a	n/a
5	SIN3A	chr21:46494706-46495676	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr21:46493543-46495715	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr21:46493607-46495487	HEK293	kidney:	n/a	n/a
8	POLR2A	chr21:46493408-46495654	K562	blood:	n/a	n/a
9	POLR2A	chr21:46493379-46495527	K562	blood:	n/a	n/a
10	RFX5	chr21:46495384-46496715	Hela-S3	cervix:	n/a	n/a
11	HEY1	chr21:46493480-46495777	K562	blood:	n/a	chr21:46494290-46494305 chr21:46494988-46495003 chr21:46494931-46494946 chr21:46494197-46494212 chr21:46495443-46495458 chr21:46494236-46494251 chr21:46494206-46494221
12	POLR2A	chr21:46494921-46495696	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr21:46492353-46497285	IMR90	lung:	n/a	n/a
14	MXI1	chr21:46494865-46495742	Hela-S3	cervix:	n/a	n/a
15	MAX	chr21:46493553-46495472	HepG2	liver:	n/a	n/a
16	RCOR1	chr21:46494724-46495774	K562	blood:	n/a	n/a
17	MAZ	chr21:46492951-46495586	IMR90	lung:	n/a	n/a
18	MAX	chr21:46494798-46495453	A549	lung:	n/a	n/a
19	POLR2A	chr21:46495305-46495420	GM12878	blood:	n/a	n/a
20	POLR2A	chr21:46493064-46495631	K562	blood:	n/a	n/a
21	FOXP2	chr21:46494886-46495449	PFSK-1	brain:	n/a	n/a
22	YY1	chr21:46494877-46495459	K562	blood:	n/a	n/a
23	POLR2A	chr21:46493574-46495510	ECC-1	luminal epithelium:	n/a	n/a
24	SMARCB1	chr21:46493611-46495619	Hela-S3	cervix:	n/a	n/a
25	GATA2	chr21:46493959-46495415	K562	blood:	n/a	n/a
26	HDAC2	chr21:46494830-46495666	MCF-7	breast:	n/a	n/a
27	MAX	chr21:46494914-46495454	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr21:46493353-46495580	K562	blood:	n/a	n/a
29	UBTF	chr21:46493360-46495761	K562	blood:	n/a	n/a
30	POLR2A	chr21:46493958-46495636	H1-neurons	neurons:	n/a	n/a
31	EBF1	chr21:46494889-46495456	GM12878	blood:	n/a	chr21:46495207-46495218 chr21:46495208-46495217 chr21:46495206-46495219 chr21:46495208-46495217 chr21:46495208-46495218
32	BACH1	chr21:46494113-46495614	H1-hESC	embryonic stem cell:	n/a	n/a
33	SIN3A	chr21:46495123-46495499	GM12878	blood:	n/a	n/a
34	NRF1	chr21:46493975-46495475	SK-N-SH	brain:	n/a	chr21:46494311-46494320 chr21:46494208-46494217
35	POLR2A	chr21:46493294-46495522	K562	blood:	n/a	n/a
36	POLR2A	chr21:46493667-46495492	MCF-7	breast:	n/a	n/a
37	POLR2A	chr21:46495293-46495427	ProgFib	skin:	n/a	n/a
38	ELF1	chr21:46494685-46495662	GM12878	blood:	n/a	chr21:46495240-46495252 chr21:46495277-46495289 chr21:46494931-46494943
39	MXI1	chr21:46494984-46495546	GM12878	blood:	n/a	n/a
40	POLR2A	chr21:46495031-46495766	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr21:46493558-46495564	ECC-1	luminal epithelium:	n/a	n/a
42	MYC	chr21:46493416-46495615	K562	blood:	n/a	n/a
43	CTCF	chr21:46495248-46495411	MCF-7	breast:	n/a	n/a
44	ZNF263	chr21:46494852-46495599	HEK293-T-REx	kidney:	n/a	n/a
45	SETDB1	chr21:46494717-46495514	K562	blood:	n/a	n/a
46	MYC	chr21:46495159-46495535	HUVEC	blood vessel:	n/a	n/a
47	RAD21	chr21:46494705-46495668	IMR90	lung:	n/a	chr21:46495353-46495363
48	POLR2A	chr21:46493392-46495615	HepG2	liver:	n/a	n/a
49	YY1	chr21:46494955-46495405	HepG2	liver:	n/a	n/a
50	HDAC2	chr21:46495254-46495605	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr21:46495389-46495439	HepG2	liver:	n/a
2	chr21:46495389-46495439	ovcar-3	ovarian:	n/a
3	chr21:46495389-46495439	GM12878	blood:	n/a
4	chr21:46495389-46495439	HPAEpiC	pulmonary alveolar:	n/a
5	chr21:46495389-46495439	SK-N-MC	brain:	n/a
6	chr21:46495389-46495439	Hela-S3	cervix:	n/a
7	chr21:46495389-46495439	SKMC	muscle:	n/a
8	chr21:46495389-46495439	AoSMC	blood vessel:	n/a
9	chr21:46495389-46495439	T-47D	breast:	n/a
10	chr21:46495389-46495439	CMK	blood:	n/a
11	chr21:46495389-46495439	ProgFib	skin:	n/a
12	chr21:46495389-46495439	HAEpiC	amniotic membrane:	n/a
13	chr21:46495389-46495439	NT2-D1	testis:	n/a
14	chr21:46495389-46495439	IMR90	lung:	fetal
15	chr21:46495389-46495439	HCF	heart:	n/a
16	chr21:46495389-46495439	HRPEpiC	eye:	n/a
17	chr21:46495389-46495439	K562	blood:	n/a
18	chr21:46495389-46495439	HRE	kidney:	n/a
19	chr21:46495389-46495439	HUVEC	blood vessel:	n/a
20	chr21:46495389-46495439	ECC-1	luminal epithelium:	n/a
21	chr21:46495389-46495439	BJ	skin:	n/a
22	chr21:46495389-46495439	SK-N-SH_RA	brain:	n/a
23	chr21:46495389-46495439	HRCEpiC	kidney:	n/a
24	chr21:46495389-46495439	AG09309	skin:	n/a
25	chr21:46495389-46495439	Jurkat	blood:	n/a
26	chr21:46495389-46495439	PrEC	prostate:	n/a
27	chr21:46495389-46495439	PFSK-1	brain:	n/a
28	chr21:46495389-46495439	GM12891	blood:	n/a
29	chr21:46495389-46495439	SAEC	small airway:	n/a
30	chr21:46495389-46495439	AG04450	lung:	fetal
31	chr21:46495389-46495439	GM06990	blood:	n/a
32	chr21:46495389-46495439	NHDF-neo	bronchial:	n/a
33	chr21:46495389-46495439	RPTEC	kidney:	n/a
34	chr21:46495389-46495439	HCM	heart:	n/a
35	chr21:46495389-46495439	MCF10A-Er-Src	breast:	n/a
36	chr21:46495389-46495439	BE2_C	brain:	n/a
37	chr21:46495389-46495439	GM19239	blood:	n/a
38	chr21:46495389-46495439	HEK293	kidney:	embryo
39	chr21:46495389-46495439	AG09319	gingival:	n/a
40	chr21:46495389-46495439	Caco-2	colon:	n/a
41	chr21:46495389-46495439	HCT-116	colon:	n/a
42	chr21:46495389-46495439	HIPEpiC	eye:	n/a
43	chr21:46495389-46495439	HMEC	breast:	n/a
44	chr21:46495389-46495439	H1-hESC	embryonic stem cell:	embryo
45	chr21:46495389-46495439	U87	brain:	n/a
46	chr21:46495389-46495439	NB4	blood:	n/a
47	chr21:46495389-46495439	NHBE	bronchial:	n/a
48	chr21:46495389-46495439	HEEpiC	esophagus:	n/a
49	chr21:46495389-46495439	HL-60	blood:	n/a
50	chr21:46495389-46495439	AG04449	skin:	fetal

(count:49 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65663723..65666241-chr21:46495274..46498090,2	K562	blood:
2	chr21:46495151..46497006-chr21:46906877..46909626,2	K562	blood:
3	chr21:46494891..46496808-chr21:46543893..46546977,3	K562	blood:
4	chr14:31495841..31497461-chr21:46493757..46496010,2	K562	blood:
5	chr21:46494888..46496545-chr21:46914062..46916067,2	K562	blood:
6	chr21:46231513..46241255-chr21:46492035..46497390,26	K562	blood:
7	chr21:46348854..46378176-chr21:46489799..46500436,75	K562	blood:
8	chr21:46363747..46379047-chr21:46484156..46498795,67	K562	blood:
9	chr21:46492248..46501057-chr21:46545477..46562980,48	K562	blood:
10	chr1:115300107..115301819-chr21:46494563..46496100,2	K562	blood:
11	chr21:46220974..46223825-chr21:46494380..46498218,5	MCF-7	breast:
12	chr21:46231904..46241990-chr21:46492035..46500735,28	K562	blood:
13	chr21:46355061..46362857-chr21:46490375..46496482,13	K562	blood:
14	chr21:46493165..46495720-chr21:46513762..46518212,6	MCF-7	breast:
15	chr21:46493210..46496355-chr21:46960101..46962644,7	K562	blood:
16	chr21:46494805..46496748-chr21:46849949..46852672,3	K562	blood:
17	chr21:46494831..46496533-chr21:46576092..46578670,2	K562	blood:
18	chr21:46492507..46498258-chr21:46706665..46711571,8	K562	blood:
19	chr21:46220151..46222677-chr21:46492186..46495962,3	K562	blood:
20	chr21:46420509..46434696-chr21:46492036..46497081,20	K562	blood:
21	chr21:46382465..46395146-chr21:46491921..46496809,22	K562	blood:
22	chr21:46387463..46395588-chr21:46492597..46498092,12	K562	blood:
23	chr1:21112741..21113311-chr21:46495175..46495793,2	Hela-S3	cervix:
24	chr21:46492924..46497122-chr21:46547379..46551295,4	MCF-7	breast:
25	chr21:46345821..46352717-chr21:46492682..46495835,7	MCF-7	breast:
26	chr21:44393563..44395189-chr21:46493572..46495769,2	K562	blood:
27	chr21:45553290..45555675-chr21:46493657..46496135,2	K562	blood:
28	chr21:46493602..46496021-chr6:27113430..27116414,2	K562	blood:
29	chr1:16840594..16842106-chr21:46494370..46496112,2	K562	blood:
30	chr21:46493904..46495468-chr21:46952040..46954795,2	K562	blood:
31	chr21:46390745..46393297-chr21:46494598..46497120,2	MCF-7	breast:
32	chr21:46493837..46495534-chr21:46954524..46956701,2	K562	blood:
33	chr21:46494890..46496733-chr21:46901945..46904600,2	K562	blood:
34	chr21:46422255..46425486-chr21:46493644..46496852,6	K562	blood:
35	chr21:46494846..46497722-chr21:46974690..46977147,2	K562	blood:
36	chr21:46494154..46496164-chr21:46707875..46710753,3	K562	blood:
37	chr21:46330635..46333372-chr21:46493231..46495849,2	K562	blood:
38	chr21:46494313..46497302-chr21:46514232..46516454,3	MCF-7	breast:
39	chr21:46398654..46417262-chr21:46491498..46498908,48	K562	blood:
40	chr21:46348334..46352514-chr21:46492914..46497675,5	K562	blood:
41	chr21:46495351..46497648-chr21:46516468..46519256,2	MCF-7	breast:
42	chr21:46491911..46497737-chr21:46547142..46552694,13	K562	blood:
43	chr21:46413441..46419649-chr21:46493522..46496485,6	K562	blood:
44	chr21:46235651..46239241-chr21:46493223..46495632,4	MCF-7	breast:
45	chr21:46492324..46495855-chr21:46960806..46963103,3	K562	blood:
46	chr21:46493052..46496413-chr21:46547928..46550318,5	MCF-7	breast:
47	chr21:46493097..46497182-chr21:46538705..46543454,4	MCF-7	breast:
48	chr21:46493821..46495801-chr21:46704505..46706122,2	K562	blood:
49	chr21:46493459..46496695-chr21:46925543..46928917,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268856	TF binding region
SSR4P1	TF binding region
ENSG00000268856	CpG island
SSR4P1	CpG island
ENSG00000182871	Chromatin interaction
ENSG00000160199	Chromatin interaction
ENSG00000184787	Chromatin interaction
ENSG00000184900	Chromatin interaction
ENSG00000272825	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000215447	Chromatin interaction
ENSG00000234880	Chromatin interaction
ENSG00000261706	Chromatin interaction
ENSG00000127483	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000009307	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000224930	Chromatin interaction
ENSG00000160221	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000268805	Chromatin interaction
ENSG00000186866	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000261135	Chromatin interaction
ENSG00000173638	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000236519	Chromatin interaction
ENSG00000100478	Chromatin interaction
ENSG00000273027	Chromatin interaction
ENSG00000197903	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2838764	0.92[ASN][1000 genomes]
rs2838767	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838768	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838770	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28760601	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8132098	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][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	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv834110	chr21:46316183-46505151	Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
3	esv3355416	chr21:46492024-46497122	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	esv3409662	chr21:46492949-46495497	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	esv3342735	chr21:46493424-46495897	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	45 gene(s)	inside rSNPs	diseases
6	esv3325657	chr21:46493549-46496097	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	45 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	chr21:46493200-46495400	Active TSS	Fetal Brain Female	brain
2	chr21:46493200-46495400	Active TSS	NHLF	lung
3	chr21:46493200-46495800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr21:46493400-46495400	Active TSS	Rectal Smooth Muscle	rectum
5	chr21:46493400-46495400	Active TSS	A549	lung
6	chr21:46493400-46495600	Active TSS	Primary T cells from cord blood	blood
7	chr21:46493400-46495600	Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr21:46493400-46495800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr21:46493400-46495800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr21:46493400-46495800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr21:46493400-46496000	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr21:46493600-46495400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr21:46493600-46495400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr21:46493600-46495400	Active TSS	Brain Angular Gyrus	brain
15	chr21:46493600-46495400	Active TSS	Fetal Intestine Small	intestine
16	chr21:46493600-46495400	Active TSS	Ovary	ovary
17	chr21:46493600-46495400	Active TSS	Small Intestine	intestine
18	chr21:46493600-46495600	Active TSS	Brain Substantia Nigra	brain
19	chr21:46493600-46495600	Active TSS	Colon Smooth Muscle	Colon
20	chr21:46493600-46495600	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr21:46493600-46495600	Active TSS	NHDF-Ad	bronchial
22	chr21:46493600-46495800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr21:46493600-46495800	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr21:46493600-46495800	Active TSS	Esophagus	oesophagus
25	chr21:46493600-46495800	Active TSS	Left Ventricle	heart
26	chr21:46493600-46496200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr21:46493600-46496600	Active TSS	HSMM	muscle
28	chr21:46493600-46496800	Active TSS	Aorta	Aorta
29	chr21:46493800-46495400	Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr21:46493800-46495400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr21:46493800-46495400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr21:46493800-46495400	Active TSS	Brain Anterior Caudate	brain
33	chr21:46493800-46495400	Active TSS	Brain Cingulate Gyrus	brain
34	chr21:46493800-46495400	Active TSS	Brain Hippocampus Middle	brain
35	chr21:46493800-46495400	Weak transcription	Fetal Heart	heart
36	chr21:46493800-46495400	Active TSS	HUVEC	blood vessel
37	chr21:46493800-46495400	Active TSS	NHEK	skin
38	chr21:46493800-46495400	Active TSS	Osteobl	bone
39	chr21:46493800-46495600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr21:46493800-46495600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr21:46493800-46495600	Active TSS	Fetal Lung	lung
42	chr21:46493800-46495800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr21:46493800-46495800	Active TSS	NH-A	brain
44	chr21:46493800-46496000	Active TSS	Muscle Satellite Cultured Cells	--
45	chr21:46493800-46496000	Bivalent/Poised TSS	Thymus	Thymus
46	chr21:46493800-46496000	Active TSS	Hela-S3	cervix
47	chr21:46493800-46496000	Active TSS	HMEC	breast
48	chr21:46493800-46496200	Active TSS	HSMMtube	muscle
49	chr21:46494000-46495400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr21:46494000-46495400	Transcr. at gene 5' and 3'	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links