Variant report

Variant	rs7282723
Chromosome Location	chr21:40196987-40196988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40193156..40195802-chr21:40196323..40199129,2	K562	blood:
2	chr21:40196402..40198026-chr21:40202193..40204500,2	K562	blood:
3	chr21:40196402..40199978-chr21:40201440..40206017,5	K562	blood:
4	chr21:40189942..40191936-chr21:40195695..40197714,2	MCF-7	breast:
5	chr21:40192244..40193901-chr21:40196829..40198564,2	MCF-7	breast:
6	chr21:40195899..40197940-chr21:40205246..40206872,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1000844	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1009121	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1051420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1051475	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10854389	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11088450	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11088451	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11088452	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11088453	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11088454	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1123350	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11254	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11701191	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11701500	0.82[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11702403	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12481740	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs12482470	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12483746	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12627283	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13046853	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13047133	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13047537	0.90[ASN][1000 genomes]
rs13047745	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13048035	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13050340	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1571707	0.94[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs2070531	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2142035	0.82[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2836683	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836684	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836685	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836686	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836687	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836688	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836689	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836690	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836691	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836692	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836693	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836694	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836710	0.94[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2836711	0.82[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs6517481	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7276961	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7282444	0.82[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs762386	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs762387	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9941892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs998855	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7282723	PCP4	cis	cerebellum	SCAN
rs7282723	MX1	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40180200-40198400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr21:40181800-40197000	Strong transcription	Fetal Thymus	thymus
3	chr21:40185000-40197000	Strong transcription	Thymus	Thymus
4	chr21:40186000-40197600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr21:40186200-40197000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr21:40187000-40197400	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr21:40187000-40197400	Strong transcription	Dnd41	blood
8	chr21:40190400-40197600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr21:40191200-40197200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr21:40191400-40197400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr21:40191400-40197600	Genic enhancers	Fetal Lung	lung
12	chr21:40192000-40197200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr21:40192400-40197000	Strong transcription	NH-A	brain
14	chr21:40192600-40197000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr21:40192600-40198200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr21:40192800-40197000	Strong transcription	HSMM	muscle
17	chr21:40193000-40197600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr21:40193200-40197000	Genic enhancers	NHDF-Ad	bronchial
19	chr21:40193600-40197400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr21:40193800-40197000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr21:40193800-40197200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr21:40193800-40197200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr21:40194000-40197600	Genic enhancers	Fetal Intestine Large	intestine
24	chr21:40194200-40202800	Weak transcription	Stomach Mucosa	stomach
25	chr21:40194400-40202800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr21:40194600-40197000	Genic enhancers	HUVEC	blood vessel
27	chr21:40194600-40203200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr21:40194800-40197200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr21:40194800-40198400	Weak transcription	Brain Hippocampus Middle	brain
30	chr21:40195000-40197200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr21:40195000-40200600	Weak transcription	Brain Angular Gyrus	brain
32	chr21:40195000-40202800	Weak transcription	Psoas Muscle	Psoas
33	chr21:40195000-40212600	Weak transcription	Right Atrium	heart
34	chr21:40195200-40197400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr21:40195200-40197400	Enhancers	Rectal Smooth Muscle	rectum
36	chr21:40195200-40197400	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr21:40195200-40197800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr21:40195200-40198200	Weak transcription	Brain Substantia Nigra	brain
39	chr21:40195200-40198400	Weak transcription	Lung	lung
40	chr21:40195200-40198600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr21:40195200-40202800	Weak transcription	Colonic Mucosa	Colon
42	chr21:40195200-40202800	Weak transcription	Small Intestine	intestine
43	chr21:40195200-40202800	Weak transcription	GM12878-XiMat	blood
44	chr21:40195200-40203400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr21:40195200-40204800	Weak transcription	Aorta	Aorta
46	chr21:40195200-40213800	Weak transcription	Fetal Kidney	kidney
47	chr21:40195600-40197200	Strong transcription	Left Ventricle	heart
48	chr21:40195800-40197400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr21:40195800-40197400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr21:40195800-40202800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links