Variant report

Variant	rs2283639
Chromosome Location	chr21:40176693-40176694
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	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	RAD21	chr21:40176494-40178046	ECC-1	luminal epithelium:	n/a	chr21:40177096-40177109 chr21:40177093-40177112 chr21:40178030-40178044
4	TCF7L2	chr21:40176617-40177947	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr21:40176660-40176810	HUVEC	blood vessel:	n/a	n/a
6	USF2	chr21:40176599-40177107	Hela-S3	cervix:	n/a	chr21:40176808-40176819
7	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
8	TCF12	chr21:40176681-40178155	A549	lung:	n/a	n/a
9	CTCF	chr21:40176580-40176730	GM12865	blood:	n/a	n/a
10	CTCF	chr21:40176580-40176730	GM12868	blood:	n/a	n/a
11	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
12	CTCF	chr21:40176580-40176730	GM12864	blood:	n/a	n/a
13	E2F6	chr21:40176650-40178180	K562	blood:	n/a	chr21:40177209-40177226 chr21:40178104-40178114 chr21:40177212-40177223
14	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
15	SMARCC1	chr21:40176513-40177935	Hela-S3	cervix:	n/a	chr21:40176655-40176664
16	FOS	chr21:40176288-40177165	MCF10A-Er-Src	breast:	n/a	chr21:40176540-40176547 chr21:40176651-40176662 chr21:40176536-40176545 chr21:40176654-40176665 chr21:40176655-40176663 chr21:40176309-40176317 chr21:40176535-40176546 chr21:40176653-40176664
17	CTCF	chr21:40176640-40176790	MCF-7	breast:	n/a	n/a
18	CTCF	chr21:40176640-40176790	GM12873	blood:	n/a	n/a
19	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
20	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
21	CTCF	chr21:40176600-40176750	Caco-2	colon:	n/a	n/a
22	POLR2A	chr21:40176494-40176962	HepG2	liver:	n/a	n/a
23	CTCF	chr21:40176606-40176802	MCF-7	breast:	n/a	n/a
24	KAP1	chr21:40176666-40177759	HEK293	kidney:	n/a	n/a
25	CTCF	chr21:40176600-40176750	GM12864	blood:	n/a	n/a
26	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
27	MAX	chr21:40176586-40178175	A549	lung:	n/a	chr21:40176731-40176740 chr21:40177454-40177463 chr21:40176637-40176646 chr21:40178111-40178121 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
28	CTCF	chr21:40176640-40176790	NHEK	skin:	n/a	n/a
29	CTCF	chr21:40176319-40179110	SK-N-SH	brain:	n/a	chr21:40177982-40177995 chr21:40177095-40177108 chr21:40177092-40177110 chr21:40177520-40177533
30	POLR2A	chr21:40175924-40187316	MCF10A-Er-Src	breast:	n/a	n/a
31	CTCF	chr21:40176620-40176770	GM12875	blood:	n/a	n/a
32	MAX	chr21:40176669-40177953	HUVEC	blood vessel:	n/a	chr21:40176731-40176740 chr21:40177454-40177463 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
33	STAT3	chr21:40176556-40177115	MCF10A-Er-Src	breast:	n/a	chr21:40176858-40176869
34	CTCF	chr21:40176640-40176790	HCPEpiC	choroid plexus:	n/a	n/a
35	MAFK	chr21:40176596-40177896	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr21:40176587-40176812	MCF-7	breast:	n/a	n/a
37	CTCF	chr21:40176620-40176770	GM12871	blood:	n/a	n/a
38	CTCF	chr21:40176680-40176830	Hela-S3	cervix:	n/a	n/a
39	REST	chr21:40176561-40178021	MCF-7	breast:	n/a	chr21:40177910-40177923 chr21:40177970-40177990 chr21:40177144-40177162
40	RAD21	chr21:40176514-40178069	MCF-7	breast:	n/a	chr21:40177096-40177109 chr21:40177093-40177112 chr21:40178030-40178044
41	CTCF	chr21:40176620-40176770	GM12864	blood:	n/a	n/a
42	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
43	CTCF	chr21:40176620-40176770	HRPEpiC	eye:	n/a	n/a
44	CTCF	chr21:40176593-40176814	MCF-7	breast:	n/a	n/a
45	CHD1	chr21:40175807-40184420	IMR90	lung:	n/a	chr21:40183942-40183952
46	CTCF	chr21:40176620-40176770	GM12873	blood:	n/a	n/a
47	HCFC1	chr21:40176304-40178467	Hela-S3	cervix:	n/a	n/a
48	RCOR1	chr21:40176543-40178074	K562	blood:	n/a	n/a
49	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
50	MAX	chr21:40176585-40178038	Hela-S3	cervix:	n/a	chr21:40176731-40176740 chr21:40177454-40177463 chr21:40176637-40176646 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465

No.	Distal block	Cell Line	Cell type
1	chr21:40176403..40178101-chr21:40218059..40219647,2	K562	blood:
2	chr21:40175328..40180167-chr21:40553641..40558387,7	K562	blood:
3	chr21:40105514..40106081-chr21:40176310..40177112,2	MCF-7	breast:
4	chr2:86902482..86903131-chr21:40176151..40176774,2	MCF-7	breast:
5	chr21:40175328..40178574-chr21:40554098..40556223,3	K562	blood:
6	chr21:40176416..40179104-chr21:40257484..40260730,3	MCF-7	breast:
7	chr21:40176632..40177186-chr21:40455915..40456479,2	MCF-7	breast:
8	chr21:40176662..40177180-chr21:40510094..40510804,2	MCF-7	breast:
9	chr21:40176601..40179515-chr21:40218059..40219886,2	K562	blood:
10	chr21:40174647..40179577-chr21:40285247..40287797,5	MCF-7	breast:
11	chr21:40176416..40178956-chr21:40498284..40502065,4	MCF-7	breast:
12	chr21:40176263..40179138-chr21:40817088..40818717,2	K562	blood:
13	chr21:40175975..40176770-chr21:40394504..40395431,2	MCF-7	breast:
14	chr21:40154093..40155752-chr21:40174948..40176789,2	MCF-7	breast:

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

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1013777	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1041781	0.86[ASN][1000 genomes]
rs1041782	0.86[ASN][1000 genomes]
rs11088448	0.86[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11088449	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs1209917	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1209923	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1209925	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1209926	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1209927	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1209928	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1209929	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1209931	0.82[ASN][1000 genomes]
rs1209932	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1209933	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1209934	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1209935	0.89[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1209936	0.82[ASN][1000 genomes]
rs1209937	0.82[ASN][1000 genomes]
rs1209938	0.85[ASN][1000 genomes]
rs1209939	0.85[ASN][1000 genomes]
rs1209940	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1209942	0.86[ASN][1000 genomes]
rs1209943	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1209944	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1209945	0.86[ASN][1000 genomes]
rs1209946	0.86[ASN][1000 genomes]
rs1209947	0.85[ASN][1000 genomes]
rs12626796	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13047789	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1309152	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2070531	0.81[CEU][hapmap]
rs2283638	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs714781	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40166600-40177000	Weak transcription	Gastric	stomach
2	chr21:40169600-40176800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr21:40172000-40177000	Enhancers	HepG2	liver
4	chr21:40172600-40176800	Enhancers	K562	blood
5	chr21:40172600-40177200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr21:40173000-40176800	Weak transcription	Right Atrium	heart
7	chr21:40173400-40176800	Enhancers	Placenta	Placenta
8	chr21:40173600-40176800	Enhancers	Stomach Mucosa	stomach
9	chr21:40174400-40176800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr21:40175200-40176800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr21:40175400-40176800	Enhancers	Fetal Muscle Trunk	muscle
12	chr21:40175400-40176800	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr21:40175400-40177000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr21:40175400-40177000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr21:40175400-40177000	Enhancers	Esophagus	oesophagus
16	chr21:40175400-40177200	Enhancers	Lung	lung
17	chr21:40175800-40176800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr21:40175800-40176800	Enhancers	Fetal Stomach	stomach
19	chr21:40176000-40176800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr21:40176000-40176800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr21:40176000-40176800	Enhancers	Fetal Muscle Leg	muscle
22	chr21:40176000-40176800	Enhancers	Pancreas	Pancrea
23	chr21:40176000-40176800	Active TSS	Stomach Smooth Muscle	stomach
24	chr21:40176000-40176800	Enhancers	GM12878-XiMat	blood
25	chr21:40176000-40177000	Enhancers	Placenta Amnion	Placenta Amnion
26	chr21:40176000-40177400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr21:40176000-40177600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr21:40176200-40176800	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr21:40176200-40176800	Weak transcription	Small Intestine	intestine
30	chr21:40176200-40176800	Enhancers	HUVEC	blood vessel
31	chr21:40176200-40176800	Enhancers	NHDF-Ad	bronchial
32	chr21:40176200-40177400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr21:40176400-40176800	Enhancers	Primary hematopoietic stem cells	blood
34	chr21:40176400-40176800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr21:40176400-40176800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr21:40176400-40176800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr21:40176400-40176800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr21:40176400-40176800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr21:40176400-40176800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr21:40176400-40176800	Enhancers	Fetal Thymus	thymus
41	chr21:40176400-40176800	Flanking Active TSS	A549	lung
42	chr21:40176400-40177000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr21:40176400-40177000	Flanking Active TSS	Hela-S3	cervix
44	chr21:40176400-40177200	Enhancers	Fetal Heart	heart
45	chr21:40176400-40177400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr21:40176400-40177400	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr21:40176400-40177400	Flanking Active TSS	Fetal Intestine Small	intestine
48	chr21:40176400-40177400	Flanking Active TSS	NH-A	brain
49	chr21:40176400-40177600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr21:40176400-40177600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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