Variant report

Variant	rs2838777
Chromosome Location	chr21:46514426-46514427
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46326231..46328580-chr21:46511672..46514505,2	MCF-7	breast:
2	chr21:46494313..46497302-chr21:46514232..46516454,3	MCF-7	breast:
3	chr21:46493165..46495720-chr21:46513762..46518212,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197381	Chromatin interaction
ENSG00000235374	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11908769	0.89[AFR][1000 genomes]
rs11911694	0.89[AFR][1000 genomes]
rs17004737	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17004740	0.89[AFR][1000 genomes]
rs17004746	0.89[AFR][1000 genomes]
rs2032253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838772	0.84[ASN][1000 genomes]
rs2838775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838784	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2877003	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3171490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373249	1.00[ASN][1000 genomes]
rs375621	1.00[ASN][1000 genomes]
rs387536	1.00[ASN][1000 genomes]
rs406923	1.00[ASN][1000 genomes]
rs407157	1.00[ASN][1000 genomes]
rs412431	0.86[ASN][1000 genomes]
rs422205	0.93[ASN][1000 genomes]
rs423892	1.00[ASN][1000 genomes]
rs425176	1.00[ASN][1000 genomes]
rs437833	1.00[ASN][1000 genomes]
rs444789	1.00[ASN][1000 genomes]
rs451550	1.00[ASN][1000 genomes]
rs73230653	1.00[AMR][1000 genomes]
rs73230658	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73230662	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73230667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230679	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230681	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232640	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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	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
3	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46496600-46516200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr21:46499000-46522200	Weak transcription	NHDF-Ad	bronchial
3	chr21:46500000-46522200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr21:46502000-46515400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr21:46502000-46516000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr21:46503000-46522200	Weak transcription	Brain Angular Gyrus	brain
7	chr21:46503200-46516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr21:46503200-46516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr21:46506600-46521400	Weak transcription	NHEK	skin
10	chr21:46507600-46515200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr21:46509400-46524000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr21:46510200-46514800	Enhancers	Fetal Brain Male	brain
13	chr21:46510200-46515600	Weak transcription	K562	blood
14	chr21:46510400-46515200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr21:46510600-46519200	Enhancers	Primary B cells from peripheral blood	blood
16	chr21:46511200-46515200	Enhancers	Primary B cells from cord blood	blood
17	chr21:46511400-46515000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr21:46511600-46514800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr21:46511800-46515400	Weak transcription	Hela-S3	cervix
20	chr21:46511800-46515600	Weak transcription	HMEC	breast
21	chr21:46511800-46520200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr21:46512000-46521600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr21:46512200-46515200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr21:46512200-46515200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr21:46512200-46515800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr21:46512200-46518000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr21:46512200-46521800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr21:46512200-46522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr21:46512200-46525600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr21:46512600-46515200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr21:46512800-46514600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr21:46512800-46515000	Enhancers	Fetal Muscle Trunk	muscle
33	chr21:46512800-46516200	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr21:46512800-46520400	Enhancers	Fetal Muscle Leg	muscle
35	chr21:46513000-46514600	Enhancers	Fetal Thymus	thymus
36	chr21:46513000-46514800	Enhancers	Primary T cells from cord blood	blood
37	chr21:46513000-46515000	Enhancers	Primary hematopoietic stem cells	blood
38	chr21:46513000-46515000	Enhancers	Colon Smooth Muscle	Colon
39	chr21:46513000-46515600	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr21:46513000-46516600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr21:46513000-46516600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr21:46513000-46516600	Enhancers	Fetal Heart	heart
43	chr21:46513000-46517600	Enhancers	Primary T cells fromperipheralblood	blood
44	chr21:46513200-46529200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr21:46513400-46515400	Weak transcription	Gastric	stomach
46	chr21:46513400-46515600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr21:46513400-46518800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr21:46513400-46521600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr21:46513600-46514600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr21:46513600-46514600	Weak transcription	Esophagus	oesophagus

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