Variant report

Variant	rs2836894
Chromosome Location	chr21:40496479-40496480
allele	A/G
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	CTCF	chr21:40496400-40496550	GM12865	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40495398..40498019-chr21:40544324..40546654,2	K562	blood:
2	chr21:40176932..40179361-chr21:40495597..40497932,3	MCF-7	breast:
3	chr21:40488161..40490338-chr21:40496446..40499117,2	K562	blood:

Variant related genes	Relation type
RPL23AP12	TF binding region
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11702077	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11702158	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242948	0.82[ASN][1000 genomes]
rs2836896	0.95[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836899	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836903	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836904	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836905	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836906	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836908	0.83[ASN][1000 genomes]
rs2836909	0.81[ASN][1000 genomes]
rs2836911	0.81[ASN][1000 genomes]
rs2836918	0.83[CHB][hapmap]
rs34912726	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34989336	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4817990	0.93[ASN][1000 genomes]
rs56147949	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62224879	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7510385	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8131292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8131570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[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	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2836894	BRWD1	cis	Lymphoblastoid	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40478600-40497000	Weak transcription	Right Atrium	heart
2	chr21:40486600-40497800	Weak transcription	Thymus	Thymus
3	chr21:40487200-40497600	Weak transcription	Colonic Mucosa	Colon
4	chr21:40487800-40497600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr21:40493200-40496600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr21:40493400-40497600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr21:40493800-40497000	Weak transcription	Lung	lung
8	chr21:40493800-40497600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr21:40494000-40497600	Weak transcription	Psoas Muscle	Psoas
10	chr21:40494000-40497600	Weak transcription	Spleen	Spleen
11	chr21:40494200-40497600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr21:40494200-40497600	Weak transcription	Esophagus	oesophagus
13	chr21:40494200-40497600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr21:40494400-40496800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr21:40494400-40497000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr21:40496000-40498400	Enhancers	Dnd41	blood
17	chr21:40496200-40498000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr21:40496200-40498000	Enhancers	Fetal Heart	heart
19	chr21:40496200-40498200	Enhancers	Stomach Smooth Muscle	stomach
20	chr21:40496200-40498400	Enhancers	Fetal Muscle Leg	muscle
21	chr21:40496200-40498400	Enhancers	NHDF-Ad	bronchial
22	chr21:40496200-40498600	Enhancers	HepG2	liver
23	chr21:40496200-40498800	Enhancers	Fetal Stomach	stomach
24	chr21:40496400-40496600	Enhancers	Aorta	Aorta
25	chr21:40496400-40496600	Enhancers	Fetal Muscle Trunk	muscle
26	chr21:40496400-40497000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr21:40496400-40497600	Enhancers	Rectal Smooth Muscle	rectum
28	chr21:40496400-40498000	Enhancers	Colon Smooth Muscle	Colon
29	chr21:40496400-40498000	Enhancers	Left Ventricle	heart
30	chr21:40496400-40498400	Enhancers	Fetal Lung	lung
31	chr21:40496400-40498800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links