Variant report

Variant	rs412431
Chromosome Location	chr21:46512506-46512507
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	chr21:46493665..46495274-chr21:46510710..46513297,2	MCF-7	breast:
3	chr21:46511460..46514377-chr21:46529611..46531181,2	K562	blood:
4	chr21:46510275..46513095-chr21:46517504..46519501,2	MCF-7	breast:
5	chr21:46510851..46513233-chr21:46534115..46536382,2	K562	blood:

Variant related genes	Relation type
ENSG00000267857	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000235374	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs17004737	0.86[ASN][1000 genomes]
rs2032253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2838772	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2838775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2838777	0.86[ASN][1000 genomes]
rs2838779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2838780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2838784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2838785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3171490	0.86[ASN][1000 genomes]
rs373249	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs375621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs387536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs406923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs407157	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs420499	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs422205	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs423892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs425176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs437833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs444789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs451550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73230667	0.86[ASN][1000 genomes]
rs73230670	0.86[ASN][1000 genomes]
rs73230679	0.86[ASN][1000 genomes]
rs73230680	0.86[ASN][1000 genomes]
rs73230681	0.86[ASN][1000 genomes]
rs73232640	0.86[ASN][1000 genomes]
rs8133767	1.00[CHB][hapmap];1.00[JPT][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	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:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46496400-46513000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr21:46496600-46516200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr21:46498600-46513000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr21:46499000-46522200	Weak transcription	NHDF-Ad	bronchial
5	chr21:46500000-46522200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr21:46501600-46513000	Weak transcription	Brain Anterior Caudate	brain
7	chr21:46502000-46515400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr21:46502000-46516000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr21:46503000-46522200	Weak transcription	Brain Angular Gyrus	brain
10	chr21:46503200-46516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr21:46503200-46516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr21:46503800-46513000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr21:46506600-46513000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr21:46506600-46521400	Weak transcription	NHEK	skin
15	chr21:46507600-46513000	Weak transcription	Esophagus	oesophagus
16	chr21:46507600-46513600	Weak transcription	Thymus	Thymus
17	chr21:46507600-46515200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr21:46508000-46513000	Weak transcription	Fetal Thymus	thymus
19	chr21:46508200-46513000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr21:46508400-46513200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr21:46509000-46512800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr21:46509000-46513000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr21:46509000-46513000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr21:46509000-46513000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr21:46509200-46512800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr21:46509400-46524000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr21:46509800-46513800	Enhancers	Fetal Brain Female	brain
28	chr21:46510000-46513200	Weak transcription	Dnd41	blood
29	chr21:46510200-46514800	Enhancers	Fetal Brain Male	brain
30	chr21:46510200-46515600	Weak transcription	K562	blood
31	chr21:46510400-46512800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr21:46510400-46513000	Weak transcription	Primary T cells from cord blood	blood
33	chr21:46510400-46515200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr21:46510600-46513200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr21:46510600-46519200	Enhancers	Primary B cells from peripheral blood	blood
36	chr21:46510800-46513000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr21:46510800-46513000	Weak transcription	Aorta	Aorta
38	chr21:46511200-46512800	Enhancers	HUVEC	blood vessel
39	chr21:46511200-46513600	Enhancers	HSMMtube	muscle
40	chr21:46511200-46515200	Enhancers	Primary B cells from cord blood	blood
41	chr21:46511400-46513000	Enhancers	Adipose Nuclei	Adipose
42	chr21:46511400-46513000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr21:46511400-46515000	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr21:46511600-46514000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr21:46511600-46514800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr21:46511800-46513000	Weak transcription	Colon Smooth Muscle	Colon
47	chr21:46511800-46513000	Weak transcription	Fetal Heart	heart
48	chr21:46511800-46513200	Weak transcription	Colonic Mucosa	Colon
49	chr21:46511800-46515400	Weak transcription	Hela-S3	cervix
50	chr21:46511800-46515600	Weak transcription	HMEC	breast

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