Variant report

Variant	rs2836706
Chromosome Location	chr21:40211489-40211490
allele	A/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40207571..40212513-chr21:40281866..40285274,6	MCF-7	breast:
2	chr21:40203275..40206794-chr21:40210041..40212530,5	MCF-7	breast:
3	chr21:40176595..40179182-chr21:40208823..40211776,3	K562	blood:
4	chr21:40175934..40178688-chr21:40209789..40212200,2	MCF-7	breast:
5	chr21:40205616..40208986-chr21:40210258..40212560,3	MCF-7	breast:
6	chr21:40206775..40209110-chr21:40210646..40213517,2	K562	blood:
7	chr21:40210912..40213065-chr21:40219265..40221347,3	K562	blood:
8	chr21:40209144..40212226-chr21:40213678..40216387,3	K562	blood:
9	chr21:40209378..40211862-chr21:40284823..40286804,2	MCF-7	breast:
10	chr21:40190407..40192977-chr21:40211375..40214122,2	MCF-7	breast:
11	chr21:40209482..40212563-chr21:40213470..40216289,3	MCF-7	breast:
12	chr21:40211369..40213824-chr21:40223080..40225148,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1534824	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534825	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534826	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070529	0.89[GIH][hapmap]
rs2070530	0.89[GIH][hapmap]
rs2836696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2836698	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2836699	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2836701	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2836702	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2836705	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836707	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836708	0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836709	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs457705	0.86[GIH][hapmap];0.82[MEX][hapmap]
rs460475	0.91[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs460982	0.87[GIH][hapmap]
rs461155	0.87[GIH][hapmap];0.82[MEX][hapmap]
rs462776	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs463452	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs467940	0.91[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs467985	0.91[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs468107	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs468193	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs468331	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs468456	0.89[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs468529	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs468837	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs468849	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs469180	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs469303	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs469353	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59427744	0.87[ASN][1000 genomes]
rs7276587	0.96[ASN][1000 genomes]
rs7279564	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7283959	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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
rs2836706	NDUFB2	trans	cerebellum	SCAN
rs2836706	MX1	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40195000-40212600	Weak transcription	Right Atrium	heart
2	chr21:40195200-40213800	Weak transcription	Fetal Kidney	kidney
3	chr21:40196400-40229000	Weak transcription	Right Ventricle	heart
4	chr21:40197000-40211800	Weak transcription	Esophagus	oesophagus
5	chr21:40203800-40225200	Weak transcription	Psoas Muscle	Psoas
6	chr21:40205400-40211800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr21:40209800-40212200	Enhancers	HepG2	liver
8	chr21:40209800-40212200	Enhancers	HUVEC	blood vessel
9	chr21:40210000-40212200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr21:40210000-40212400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr21:40210000-40212800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr21:40210000-40214000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr21:40210000-40214000	Enhancers	NHEK	skin
14	chr21:40210000-40214200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr21:40210000-40214200	Enhancers	HMEC	breast
16	chr21:40210200-40211800	Weak transcription	Placenta	Placenta
17	chr21:40210200-40212200	Enhancers	Fetal Muscle Trunk	muscle
18	chr21:40210200-40212400	Enhancers	NHLF	lung
19	chr21:40210200-40212800	Enhancers	NHDF-Ad	bronchial
20	chr21:40210200-40213800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr21:40210400-40212400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr21:40210400-40212400	Enhancers	HSMM	muscle
23	chr21:40210400-40212600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr21:40210400-40212800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr21:40210600-40212000	Enhancers	Fetal Stomach	stomach
26	chr21:40210600-40212200	Enhancers	HSMMtube	muscle
27	chr21:40210800-40211800	Enhancers	NH-A	brain
28	chr21:40210800-40212000	Enhancers	Small Intestine	intestine
29	chr21:40210800-40212400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr21:40211000-40212200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr21:40211000-40212200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr21:40211000-40212200	Enhancers	Fetal Muscle Leg	muscle
33	chr21:40211000-40212200	Flanking Active TSS	Osteobl	bone
34	chr21:40211200-40211600	Enhancers	Fetal Intestine Large	intestine
35	chr21:40211200-40211800	Active TSS	A549	lung
36	chr21:40211200-40211800	Enhancers	Hela-S3	cervix
37	chr21:40211200-40212000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr21:40211200-40212200	Enhancers	K562	blood
39	chr21:40211400-40211600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr21:40211400-40211600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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