Variant report

Variant	rs9975728
Chromosome Location	chr21:40662749-40662750
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40660582..40664374-chr21:40667695..40671151,4	MCF-7	breast:
2	chr21:40659858..40663971-chr21:40719417..40722470,4	MCF-7	breast:
3	chr21:40650245..40652067-chr21:40661600..40663535,2	MCF-7	breast:
4	chr21:40655412..40656996-chr21:40661795..40664076,2	MCF-7	breast:
5	chr21:40660622..40662846-chr21:40664648..40666814,2	K562	blood:
6	chr21:40647474..40653272-chr21:40661501..40665545,6	K562	blood:
7	chr21:40648027..40649939-chr21:40662663..40664806,2	K562	blood:
8	chr21:40657853..40663062-chr21:40682568..40687952,7	MCF-7	breast:
9	chr21:40661492..40663518-chr21:40759529..40761467,2	K562	blood:
10	chr21:40661282..40662846-chr21:40664648..40666203,2	K562	blood:
11	chr21:40661393..40663465-chr21:40683759..40685454,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238141	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10154073	0.84[EUR][1000 genomes]
rs1046289	0.82[AMR][1000 genomes]
rs12329720	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12329767	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2070866	0.83[EUR][1000 genomes]
rs2178838	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234545	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836936	0.82[AMR][1000 genomes]
rs2836937	0.82[AMR][1000 genomes]
rs2836941	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836946	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836947	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836962	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836963	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836970	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836976	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836978	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836979	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28397992	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28460573	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28494168	0.87[EUR][1000 genomes]
rs28542479	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28580194	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28590100	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28665841	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28684434	0.87[EUR][1000 genomes]
rs28693867	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28734946	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4818020	0.84[EUR][1000 genomes]
rs4818026	0.84[EUR][1000 genomes]
rs7278048	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7281540	0.82[AMR][1000 genomes]
rs8130083	0.83[EUR][1000 genomes]
rs9284464	0.84[EUR][1000 genomes]
rs9305673	0.83[EUR][1000 genomes]
rs997146	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9974266	0.83[EUR][1000 genomes]
rs9975256	0.87[EUR][1000 genomes]
rs9975909	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9975937	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9976346	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977787	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9977926	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979571	0.84[EUR][1000 genomes]
rs9979691	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979936	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9981349	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9981527	0.83[EUR][1000 genomes]
rs9982825	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9982870	0.84[EUR][1000 genomes]
rs9984518	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9984922	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9985067	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9985148	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[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	nsv1056683	chr21:40570023-40673210	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9975728	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs9975728	BRWD1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40608400-40667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:40630200-40662800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr21:40631200-40663600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr21:40633200-40662800	Weak transcription	Esophagus	oesophagus
5	chr21:40638200-40665000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr21:40638600-40663400	Weak transcription	Gastric	stomach
7	chr21:40638600-40663400	Weak transcription	Psoas Muscle	Psoas
8	chr21:40638600-40665600	Weak transcription	Spleen	Spleen
9	chr21:40639000-40663400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr21:40641400-40683800	Strong transcription	Placenta	Placenta
11	chr21:40643000-40662800	Weak transcription	NHLF	lung
12	chr21:40643400-40662800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr21:40643400-40662800	Weak transcription	Brain Hippocampus Middle	brain
14	chr21:40643600-40663600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr21:40643800-40684200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr21:40646600-40662800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr21:40646600-40683400	Weak transcription	Fetal Brain Male	brain
18	chr21:40647400-40663600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr21:40650200-40663400	Weak transcription	Right Ventricle	heart
20	chr21:40650200-40671600	Weak transcription	Aorta	Aorta
21	chr21:40651400-40671600	Weak transcription	Pancreas	Pancrea
22	chr21:40655000-40669400	Strong transcription	NHDF-Ad	bronchial
23	chr21:40655000-40676800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr21:40655000-40683000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr21:40655400-40683200	Strong transcription	Dnd41	blood
26	chr21:40655600-40671800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr21:40655800-40671800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr21:40655800-40672200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr21:40655800-40672800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr21:40655800-40673800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr21:40655800-40677400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr21:40655800-40677400	Strong transcription	Fetal Thymus	thymus
33	chr21:40656000-40669400	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr21:40656200-40662800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr21:40656200-40672400	Strong transcription	Liver	Liver
36	chr21:40656200-40672600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr21:40656200-40674200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr21:40656400-40670200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr21:40656400-40675400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr21:40656400-40676600	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr21:40656400-40676800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr21:40656400-40683800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr21:40656600-40662800	Weak transcription	Ovary	ovary
44	chr21:40656600-40671600	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr21:40657000-40662800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr21:40657400-40663400	Weak transcription	NHEK	skin
47	chr21:40658800-40666400	Strong transcription	Primary B cells from cord blood	blood
48	chr21:40658800-40669000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr21:40658800-40670600	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr21:40658800-40672000	Strong transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links