Variant report

Variant	rs2836701
Chromosome Location	chr21:40209798-40209799
allele	A/C
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40203421..40205161-chr21:40207870..40210107,2	MCF-7	breast:
2	chr21:40207571..40212513-chr21:40281866..40285274,6	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	chr21:40208198..40210644-chr21:40213695..40215361,2	K562	blood:
6	chr21:40208550..40210210-chr21:40331098..40333254,2	MCF-7	breast:
7	chr21:40176843..40178369-chr21:40207397..40210316,2	MCF-7	breast:
8	chr21:40205540..40207213-chr21:40208590..40210222,2	K562	blood:
9	chr21:40176450..40178743-chr21:40208823..40210480,3	K562	blood:
10	chr21:40209144..40212226-chr21:40213678..40216387,3	K562	blood:
11	chr21:40209378..40211862-chr21:40284823..40286804,2	MCF-7	breast:
12	chr21:40190146..40192879-chr21:40208219..40210251,3	MCF-7	breast:
13	chr21:40209482..40212563-chr21:40213470..40216289,3	MCF-7	breast:

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];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534825	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534826	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070529	0.91[GIH][hapmap]
rs2070530	0.91[GIH][hapmap]
rs2836696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836698	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836699	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836702	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836705	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836706	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]
rs2836707	0.95[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836708	0.95[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836709	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs457705	0.89[GIH][hapmap]
rs460475	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs460982	0.89[GIH][hapmap]
rs461155	0.89[GIH][hapmap]
rs462776	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs463452	0.90[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs467940	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs467985	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs468107	0.92[ASN][1000 genomes]
rs468193	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs468331	0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs468456	0.94[CHB][hapmap];0.91[ASN][1000 genomes]
rs468529	0.91[ASN][1000 genomes]
rs468837	0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs468849	0.95[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs469180	1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs469303	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs469353	0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59427744	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7276587	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7279564	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs7283959	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
rs2836701	CHAF1B	cis	parietal	SCAN
rs2836701	MX1	cis	cerebellum	SCAN

Chromatin state (count:22 , 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	chr21:40196600-40211000	Weak transcription	Pancreas	Pancrea
5	chr21:40197000-40211800	Weak transcription	Esophagus	oesophagus
6	chr21:40203200-40210600	Weak transcription	Spleen	Spleen
7	chr21:40203800-40225200	Weak transcription	Psoas Muscle	Psoas
8	chr21:40204200-40210200	Weak transcription	NHLF	lung
9	chr21:40204600-40210000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr21:40204600-40210000	Weak transcription	HMEC	breast
11	chr21:40204800-40209800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr21:40204800-40210000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr21:40204800-40210000	Weak transcription	NHEK	skin
14	chr21:40205000-40210000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr21:40205200-40210000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr21:40205400-40211800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr21:40205600-40210400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr21:40207000-40210400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr21:40207600-40209800	Weak transcription	HepG2	liver
20	chr21:40209600-40210200	Enhancers	Dnd41	blood
21	chr21:40209600-40210600	Enhancers	Hela-S3	cervix
22	chr21:40209600-40210800	Enhancers	K562	blood

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