Variant report

Variant	rs2838772
Chromosome Location	chr21:46501659-46501660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46500190..46501705-chr21:46518779..46520799,2	K562	blood:
2	chr21:46499894..46505152-chr21:46506062..46510299,9	MCF-7	breast:
3	chr21:46499575..46502481-chr21:46547014..46549747,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197381	Chromatin interaction

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

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

rs_ID	r²[population]
rs17004737	0.84[ASN][1000 genomes]
rs2032253	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2838757	1.00[CHB][hapmap]
rs2838775	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2838777	0.84[ASN][1000 genomes]
rs2838779	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2838780	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2838784	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2838785	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs3171490	0.84[ASN][1000 genomes]
rs373249	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs375621	1.00[CHB][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs387536	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs406923	1.00[CHB][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs407157	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs412431	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs420499	0.88[EUR][1000 genomes]
rs422205	0.92[EUR][1000 genomes]
rs423892	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs425176	1.00[CHB][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs437833	1.00[CHB][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs444789	1.00[CHB][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs451550	1.00[CHB][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73230653	0.82[ASN][1000 genomes]
rs73230658	0.82[ASN][1000 genomes]
rs73230662	1.00[ASN][1000 genomes]
rs73230667	0.84[ASN][1000 genomes]
rs73230670	0.84[ASN][1000 genomes]
rs73230679	0.84[ASN][1000 genomes]
rs73230680	0.84[ASN][1000 genomes]
rs73230681	0.84[ASN][1000 genomes]
rs73232640	0.84[ASN][1000 genomes]
rs8133767	1.00[CHB][hapmap]

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	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	nsv3541	chr21:46496415-46536629	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46495800-46502600	Weak transcription	Colonic Mucosa	Colon
2	chr21:46495800-46506000	Weak transcription	Pancreas	Pancrea
3	chr21:46496200-46506600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr21:46496200-46511600	Weak transcription	Fetal Intestine Small	intestine
5	chr21:46496400-46509000	Enhancers	Primary T cells fromperipheralblood	blood
6	chr21:46496400-46509000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr21:46496400-46511400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr21:46496400-46511400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr21:46496400-46513000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr21:46496600-46511600	Weak transcription	Brain Hippocampus Middle	brain
11	chr21:46496600-46512000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr21:46496600-46516200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr21:46497000-46502000	Genic enhancers	HSMM	muscle
14	chr21:46497000-46504600	Weak transcription	Fetal Intestine Large	intestine
15	chr21:46497600-46509200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr21:46498000-46502000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr21:46498000-46509200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr21:46498200-46502000	Enhancers	Fetal Thymus	thymus
19	chr21:46498200-46502000	Enhancers	Left Ventricle	heart
20	chr21:46498400-46501800	Enhancers	Spleen	Spleen
21	chr21:46498600-46502800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr21:46498600-46513000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr21:46499000-46506600	Weak transcription	Fetal Brain Male	brain
24	chr21:46499000-46522200	Weak transcription	NHDF-Ad	bronchial
25	chr21:46499800-46501800	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr21:46499800-46507000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr21:46499800-46509200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr21:46499800-46510400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr21:46500000-46501800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr21:46500000-46506800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr21:46500000-46522200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr21:46500200-46503000	Enhancers	Rectal Smooth Muscle	rectum
33	chr21:46500400-46503000	Weak transcription	Psoas Muscle	Psoas
34	chr21:46500600-46501800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr21:46500600-46501800	Enhancers	NHLF	lung
36	chr21:46500800-46501800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr21:46500800-46501800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr21:46500800-46508800	Weak transcription	Fetal Brain Female	brain
39	chr21:46501000-46501800	Genic enhancers	Aorta	Aorta
40	chr21:46501000-46502000	Genic enhancers	Esophagus	oesophagus
41	chr21:46501000-46502200	Strong transcription	Adipose Nuclei	Adipose
42	chr21:46501000-46502400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr21:46501000-46502800	Strong transcription	Fetal Muscle Leg	muscle
44	chr21:46501000-46503000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr21:46501000-46503000	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr21:46501000-46503000	Strong transcription	HepG2	liver
47	chr21:46501000-46506800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr21:46501000-46509000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr21:46501200-46501800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr21:46501200-46501800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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