Variant report

Variant	rs2283638
Chromosome Location	chr21:40176111-40176112
allele	A/C
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	POLR2A	chr21:40175826-40184443	MCF10A-Er-Src	breast:	n/a	n/a
2	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
3	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
4	POLR2A	chr21:40175924-40187316	MCF10A-Er-Src	breast:	n/a	n/a
5	CHD1	chr21:40175807-40184420	IMR90	lung:	n/a	chr21:40183942-40183952
6	POLR2A	chr21:40176087-40184309	IMR90	lung:	n/a	n/a
7	POLR2A	chr21:40175758-40179245	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr21:40176048-40176261	MCF-7	breast:	n/a	n/a

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	chr21:40174647..40179577-chr21:40285247..40287797,5	MCF-7	breast:
4	chr21:40174974..40176584-chr21:40544801..40546577,2	K562	blood:
5	chr21:40175975..40176770-chr21:40394504..40395431,2	MCF-7	breast:
6	chr21:40154093..40155752-chr21:40174948..40176789,2	MCF-7	breast:

Variant related genes	Relation type
ETS2	TF binding region
ENSG00000234035	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000183527	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1013777	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1041781	0.87[ASN][1000 genomes]
rs1041782	0.87[ASN][1000 genomes]
rs11088448	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11088449	0.90[EUR][1000 genomes]
rs1209917	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1209923	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1209925	0.87[CHB][hapmap];0.86[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	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs1209931	0.82[ASN][1000 genomes]
rs1209932	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1209933	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1209934	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1209935	0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1209936	0.83[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	0.87[ASN][1000 genomes]
rs1209943	0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs1209944	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1209945	0.87[ASN][1000 genomes]
rs1209946	0.87[ASN][1000 genomes]
rs1209947	0.86[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];0.98[ASN][1000 genomes]
rs1309152	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2283639	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:3 , 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

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40165000-40176600	Enhancers	Fetal Intestine Large	intestine
2	chr21:40166600-40177000	Weak transcription	Gastric	stomach
3	chr21:40167000-40176600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr21:40169600-40176800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr21:40170400-40176600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr21:40170800-40176400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr21:40171200-40176600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr21:40171400-40176400	Weak transcription	Hela-S3	cervix
9	chr21:40172000-40177000	Enhancers	HepG2	liver
10	chr21:40172600-40176800	Enhancers	K562	blood
11	chr21:40172600-40177200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr21:40173000-40176800	Weak transcription	Right Atrium	heart
13	chr21:40173400-40176800	Enhancers	Placenta	Placenta
14	chr21:40173600-40176800	Enhancers	Stomach Mucosa	stomach
15	chr21:40173800-40176600	Weak transcription	HMEC	breast
16	chr21:40174000-40176200	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr21:40174000-40176400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr21:40174000-40176400	Enhancers	Duodenum Mucosa	Duodenum
19	chr21:40174200-40176600	Enhancers	Fetal Lung	lung
20	chr21:40174400-40176600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr21:40174400-40176800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr21:40174600-40176200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr21:40175200-40176800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr21:40175400-40176200	Enhancers	Primary hematopoietic stem cells	blood
25	chr21:40175400-40176200	Genic enhancers	Fetal Intestine Small	intestine
26	chr21:40175400-40176200	Weak transcription	Osteobl	bone
27	chr21:40175400-40176600	Enhancers	NHEK	skin
28	chr21:40175400-40176800	Enhancers	Fetal Muscle Trunk	muscle
29	chr21:40175400-40176800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr21:40175400-40177000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr21:40175400-40177000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr21:40175400-40177000	Enhancers	Esophagus	oesophagus
33	chr21:40175400-40177200	Enhancers	Lung	lung
34	chr21:40175800-40176400	Enhancers	NH-A	brain
35	chr21:40175800-40176800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr21:40175800-40176800	Enhancers	Fetal Stomach	stomach
37	chr21:40176000-40176200	Flanking Active TSS	Colonic Mucosa	Colon
38	chr21:40176000-40176200	Enhancers	Psoas Muscle	Psoas
39	chr21:40176000-40176200	Enhancers	Small Intestine	intestine
40	chr21:40176000-40176400	Enhancers	Brain Anterior Caudate	brain
41	chr21:40176000-40176400	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr21:40176000-40176400	Enhancers	A549	lung
43	chr21:40176000-40176600	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr21:40176000-40176600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr21:40176000-40176600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr21:40176000-40176600	Weak transcription	NHLF	lung
47	chr21:40176000-40176800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
48	chr21:40176000-40176800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr21:40176000-40176800	Enhancers	Fetal Muscle Leg	muscle
50	chr21:40176000-40176800	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links