Variant report

Variant	rs2000639
Chromosome Location	chr21:40280522-40280523
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40270467..40272211-chr21:40279287..40280872,2	MCF-7	breast:
2	chr21:40191292..40193852-chr21:40279000..40281951,2	MCF-7	breast:
3	chr21:40168506..40170347-chr21:40280302..40282000,2	MCF-7	breast:
4	chr21:40276535..40278972-chr21:40279958..40281891,2	K562	blood:
5	chr21:40173449..40180758-chr21:40275825..40282486,14	MCF-7	breast:
6	chr21:40280234..40282411-chr21:40330547..40333057,2	MCF-7	breast:
7	chr21:40274625..40276194-chr21:40279774..40282336,2	K562	blood:
8	chr21:40267221..40269105-chr21:40280322..40281835,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10854390	0.88[EUR][1000 genomes]
rs11909298	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12481753	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12482288	0.88[EUR][1000 genomes]
rs12483491	0.88[EUR][1000 genomes]
rs13048952	0.88[EUR][1000 genomes]
rs13050477	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13051097	0.83[EUR][1000 genomes]
rs13339960	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2094873	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2410064	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2836718	0.92[CEU][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.82[EUR][1000 genomes]
rs2836719	0.83[EUR][1000 genomes]
rs2836735	0.92[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2836737	0.92[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2836740	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2836746	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs34578621	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4143382	0.83[EUR][1000 genomes]
rs4817966	0.83[EUR][1000 genomes]
rs7275316	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7275685	0.88[EUR][1000 genomes]
rs7277330	0.82[EUR][1000 genomes]
rs7278979	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7279223	0.83[EUR][1000 genomes]
rs8126904	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8131220	0.88[EUR][1000 genomes]
rs9680142	0.82[EUR][1000 genomes]
rs9680143	0.92[CEU][hapmap];0.83[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2000639	ITSN1	cis	parietal	SCAN
rs2000639	DSCR6	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40273800-40284800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr21:40277800-40281200	Enhancers	Hela-S3	cervix
3	chr21:40277800-40287000	Enhancers	Left Ventricle	heart
4	chr21:40278000-40283400	Enhancers	Placenta	Placenta
5	chr21:40278400-40284800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr21:40278600-40280600	Enhancers	Placenta Amnion	Placenta Amnion
7	chr21:40278600-40281200	Enhancers	HMEC	breast
8	chr21:40278600-40282600	Enhancers	Spleen	Spleen
9	chr21:40278600-40283000	Enhancers	Fetal Intestine Small	intestine
10	chr21:40278600-40283600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr21:40278600-40284600	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr21:40278600-40284800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr21:40278600-40285000	Enhancers	NHEK	skin
14	chr21:40278600-40285200	Enhancers	Right Ventricle	heart
15	chr21:40278800-40284400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr21:40279000-40280800	Weak transcription	Ovary	ovary
17	chr21:40279000-40280800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr21:40279000-40281800	Weak transcription	Colonic Mucosa	Colon
19	chr21:40279400-40280600	Weak transcription	Lung	lung
20	chr21:40279400-40280800	Enhancers	Aorta	Aorta
21	chr21:40279400-40281600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr21:40279400-40282200	Weak transcription	HSMMtube	muscle
23	chr21:40279400-40284800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr21:40279600-40280600	Enhancers	Fetal Heart	heart
25	chr21:40279600-40280600	Weak transcription	Fetal Thymus	thymus
26	chr21:40279600-40280600	Weak transcription	Right Atrium	heart
27	chr21:40279600-40280800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr21:40279600-40280800	Enhancers	Duodenum Mucosa	Duodenum
29	chr21:40279600-40280800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr21:40279600-40280800	Weak transcription	Pancreas	Pancrea
31	chr21:40279600-40281200	Weak transcription	Fetal Muscle Leg	muscle
32	chr21:40279600-40281600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr21:40279600-40282400	Weak transcription	HSMM	muscle
34	chr21:40279600-40282600	Weak transcription	Psoas Muscle	Psoas
35	chr21:40279600-40282800	Enhancers	Small Intestine	intestine
36	chr21:40279600-40283400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr21:40279600-40285600	Weak transcription	Fetal Kidney	kidney
38	chr21:40279800-40282200	Weak transcription	A549	lung
39	chr21:40279800-40282600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr21:40279800-40282600	Weak transcription	Liver	Liver
41	chr21:40279800-40285000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr21:40279800-40285600	Weak transcription	NHDF-Ad	bronchial
43	chr21:40280000-40280800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr21:40280000-40281400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr21:40280000-40281600	Weak transcription	Fetal Lung	lung
46	chr21:40280000-40284000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr21:40280200-40280600	Weak transcription	HepG2	liver
48	chr21:40280200-40282000	Weak transcription	Fetal Intestine Large	intestine
49	chr21:40280200-40282600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr21:40280200-40284600	Weak transcription	Colon Smooth Muscle	Colon

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