Variant report

Variant	rs16996809
Chromosome Location	chr21:40139414-40139415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40138076..40140463-chr21:40532005..40534792,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs16996783	1.00[AMR][1000 genomes]
rs2156421	1.00[AMR][1000 genomes]
rs2836674	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2836675	0.93[LWK][hapmap];0.86[MKK][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59340988	1.00[AMR][1000 genomes]
rs60357523	1.00[AMR][1000 genomes]
rs73440499	1.00[AMR][1000 genomes]
rs73442430	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060405	chr21:40095523-40159813	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1057356	chr21:40103881-40147363	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv913739	chr21:40103951-40152372	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv913740	chr21:40103951-40157124	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1066051	chr21:40114130-40147363	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1057627	chr21:40114130-40151977	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1060535	chr21:40114130-40155067	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1063936	chr21:40114130-40159150	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1058591	chr21:40114130-40190594	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv913741	chr21:40116044-40142854	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv459254	chr21:40116044-40152372	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv459255	chr21:40116044-40152372	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv459256	chr21:40116044-40152372	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv459257	chr21:40116044-40152372	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv470900	chr21:40116044-40152372	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv587475	chr21:40116044-40152372	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv459258	chr21:40116044-40157124	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv587476	chr21:40116044-40157124	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv913742	chr21:40116044-40157124	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv516348	chr21:40116044-40161381	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
21	nsv913743	chr21:40116044-40161381	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
22	nsv1055623	chr21:40118451-40161072	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv1056485	chr21:40128875-40159813	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40128200-40144600	Weak transcription	Hela-S3	cervix
2	chr21:40130000-40140400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr21:40132600-40144800	Weak transcription	Aorta	Aorta
4	chr21:40132600-40144800	Weak transcription	Ovary	ovary
5	chr21:40133800-40140400	Weak transcription	NHDF-Ad	bronchial
6	chr21:40138400-40141000	Enhancers	Stomach Mucosa	stomach
7	chr21:40138800-40139600	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr21:40138800-40139600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr21:40138800-40139600	Active TSS	Primary T cells from cord blood	blood
10	chr21:40138800-40139600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr21:40138800-40139600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr21:40138800-40139600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr21:40138800-40139600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr21:40138800-40139600	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr21:40138800-40139600	Active TSS	Adipose Nuclei	Adipose
16	chr21:40138800-40139600	Active TSS	Colonic Mucosa	Colon
17	chr21:40138800-40139600	Flanking Active TSS	Fetal Intestine Small	intestine
18	chr21:40138800-40139600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr21:40138800-40139600	Active TSS	Thymus	Thymus
20	chr21:40138800-40139800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr21:40138800-40139800	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr21:40138800-40139800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr21:40138800-40139800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr21:40138800-40139800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr21:40138800-40139800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr21:40138800-40139800	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr21:40138800-40139800	Active TSS	Rectal Smooth Muscle	rectum
28	chr21:40138800-40140000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr21:40138800-40140000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr21:40138800-40140200	Flanking Active TSS	Dnd41	blood
31	chr21:40138800-40141200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr21:40139000-40139600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr21:40139000-40139600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr21:40139000-40139600	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr21:40139000-40139600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr21:40139000-40139600	Active TSS	Brain Angular Gyrus	brain
37	chr21:40139000-40139600	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr21:40139000-40139600	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr21:40139000-40139800	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr21:40139000-40139800	Flanking Active TSS	NHEK	skin
41	chr21:40139200-40139600	Active TSS	Primary B cells from cord blood	blood
42	chr21:40139200-40139600	Active TSS	Primary B cells from peripheral blood	blood
43	chr21:40139200-40139600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr21:40139200-40139600	Active TSS	Duodenum Mucosa	Duodenum
45	chr21:40139200-40139600	Active TSS	Fetal Thymus	thymus
46	chr21:40139200-40139600	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr21:40139200-40139600	Active TSS	Right Atrium	heart
48	chr21:40139200-40139600	Active TSS	GM12878-XiMat	blood
49	chr21:40139200-40139600	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr21:40139200-40139800	Active TSS	Primary T cells fromperipheralblood	blood

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