Variant report

Variant	rs2836683
Chromosome Location	chr21:40197438-40197439
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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1009121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1051420	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1051475	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1051476	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10854389	0.89[ASN][1000 genomes]
rs11088450	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11088451	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11088452	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11088453	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11088454	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1123350	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11254	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11701191	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11701500	0.94[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11702403	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12481740	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs12482470	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12483746	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12627283	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13046853	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13047133	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13047537	0.89[ASN][1000 genomes]
rs13047745	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13048035	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13050340	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1571707	0.94[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs2070531	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2142035	0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2836684	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836685	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836686	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836687	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836688	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836689	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836690	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836691	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836692	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836693	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836710	0.94[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs2836711	0.94[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs6517481	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7276961	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7282444	0.94[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs7282723	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762386	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs762387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9941892	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs998855	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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
rs2836683	PCP4	cis	cerebellum	SCAN
rs2836683	MX1	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40180200-40198400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr21:40186000-40197600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr21:40190400-40197600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr21:40191400-40197600	Genic enhancers	Fetal Lung	lung
5	chr21:40192600-40198200	Weak transcription	Primary B cells from peripheral blood	blood
6	chr21:40193000-40197600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr21:40194000-40197600	Genic enhancers	Fetal Intestine Large	intestine
8	chr21:40194200-40202800	Weak transcription	Stomach Mucosa	stomach
9	chr21:40194400-40202800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr21:40194600-40203200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr21:40194800-40198400	Weak transcription	Brain Hippocampus Middle	brain
12	chr21:40195000-40200600	Weak transcription	Brain Angular Gyrus	brain
13	chr21:40195000-40202800	Weak transcription	Psoas Muscle	Psoas
14	chr21:40195000-40212600	Weak transcription	Right Atrium	heart
15	chr21:40195200-40197800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr21:40195200-40198200	Weak transcription	Brain Substantia Nigra	brain
17	chr21:40195200-40198400	Weak transcription	Lung	lung
18	chr21:40195200-40198600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr21:40195200-40202800	Weak transcription	Colonic Mucosa	Colon
20	chr21:40195200-40202800	Weak transcription	Small Intestine	intestine
21	chr21:40195200-40202800	Weak transcription	GM12878-XiMat	blood
22	chr21:40195200-40203400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr21:40195200-40204800	Weak transcription	Aorta	Aorta
24	chr21:40195200-40213800	Weak transcription	Fetal Kidney	kidney
25	chr21:40195800-40202800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr21:40196000-40198000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr21:40196200-40198000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr21:40196200-40198000	Enhancers	HepG2	liver
29	chr21:40196400-40198400	Weak transcription	Primary B cells from cord blood	blood
30	chr21:40196400-40202800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr21:40196400-40206600	Weak transcription	Gastric	stomach
32	chr21:40196400-40229000	Weak transcription	Right Ventricle	heart
33	chr21:40196600-40197600	Strong transcription	Primary hematopoietic stem cells	blood
34	chr21:40196600-40197600	Enhancers	Fetal Stomach	stomach
35	chr21:40196600-40197800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr21:40196600-40197800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr21:40196600-40198200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr21:40196600-40198200	Weak transcription	Brain Anterior Caudate	brain
39	chr21:40196600-40198200	Weak transcription	HMEC	breast
40	chr21:40196600-40199000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr21:40196600-40200600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr21:40196600-40202800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr21:40196600-40202800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr21:40196600-40202800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr21:40196600-40202800	Weak transcription	Hela-S3	cervix
46	chr21:40196600-40202800	Weak transcription	K562	blood
47	chr21:40196600-40202800	Weak transcription	NHEK	skin
48	chr21:40196600-40203000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr21:40196600-40203000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr21:40196600-40203000	Weak transcription	Muscle Satellite Cultured Cells	--

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