Variant report

Variant	rs2410062
Chromosome Location	chr21:40228920-40228921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40227190..40230655-chr21:40232406..40235410,3	K562	blood:
2	chr21:40227996..40231150-chr21:40232050..40235725,3	MCF-7	breast:
3	chr21:40227300..40229882-chr21:40259597..40261140,2	MCF-7	breast:
4	chr21:40225549..40227156-chr21:40227645..40229389,2	K562	blood:
5	chr21:40176981..40179168-chr21:40228502..40230846,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229925	Chromatin interaction
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11701301	0.96[ASN][1000 genomes]
rs11911369	0.85[ASN][1000 genomes]
rs17230954	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17230961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298560	1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2836715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2836717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2836720	0.96[ASN][1000 genomes]
rs2836724	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28420538	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs28508188	0.96[ASN][1000 genomes]
rs28817686	0.96[ASN][1000 genomes]
rs28836833	0.96[ASN][1000 genomes]
rs414845	0.82[JPT][hapmap]
rs456508	0.91[CEU][hapmap]
rs465189	0.91[CEU][hapmap]
rs465214	0.91[CEU][hapmap]
rs467698	0.96[ASN][1000 genomes]
rs467806	0.96[ASN][1000 genomes]
rs57740627	0.85[ASN][1000 genomes]
rs59086904	0.96[ASN][1000 genomes]
rs60328145	0.82[ASN][1000 genomes]
rs714780	0.85[ASN][1000 genomes]
rs7278693	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7279299	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7283433	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73450548	0.85[ASN][1000 genomes]
rs73450552	0.85[ASN][1000 genomes]
rs8127274	1.00[CHB][hapmap]
rs8128181	0.82[ASN][1000 genomes]
rs8133056	0.82[ASN][1000 genomes]
rs8133164	0.82[ASN][1000 genomes]
rs8134019	0.82[ASN][1000 genomes]
rs8134441	0.82[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	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2410062	NCRNA00257	cis	parietal	SCAN
rs2410062	MX1	cis	cerebellum	SCAN
rs2410062	ETS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40196400-40229000	Weak transcription	Right Ventricle	heart
2	chr21:40219800-40229000	Weak transcription	Right Atrium	heart
3	chr21:40220400-40229000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr21:40221200-40229000	Weak transcription	Left Ventricle	heart
5	chr21:40225800-40234400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr21:40226000-40232000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr21:40226000-40233600	Weak transcription	Spleen	Spleen
8	chr21:40226000-40242200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr21:40226200-40229200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr21:40226200-40229200	Weak transcription	Thymus	Thymus
11	chr21:40226200-40229200	Weak transcription	NH-A	brain
12	chr21:40226200-40232800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr21:40226400-40229000	Weak transcription	Dnd41	blood
14	chr21:40226400-40229800	Weak transcription	HUVEC	blood vessel
15	chr21:40226400-40230400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr21:40226400-40231800	Weak transcription	NHEK	skin
17	chr21:40228200-40230400	Enhancers	Fetal Heart	heart
18	chr21:40228200-40231000	Enhancers	Fetal Muscle Trunk	muscle
19	chr21:40228400-40229000	Enhancers	K562	blood
20	chr21:40228400-40230400	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr21:40228400-40231200	Enhancers	Fetal Muscle Leg	muscle
22	chr21:40228600-40229600	Enhancers	Psoas Muscle	Psoas
23	chr21:40228600-40230000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr21:40228800-40229000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr21:40228800-40229000	Enhancers	HepG2	liver
26	chr21:40228800-40229000	Enhancers	HSMMtube	muscle
27	chr21:40228800-40230200	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links