Variant report

Variant	rs9980120
Chromosome Location	chr21:40331605-40331606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40330886-40331617	MCF10A-Er-Src	breast:	n/a	n/a
2	JUN	chr21:40330691-40332312	K562	blood:	n/a	chr21:40331842-40331850 chr21:40331286-40331299 chr21:40331071-40331078 chr21:40331071-40331079
3	MAX	chr21:40331021-40332050	HepG2	liver:	n/a	chr21:40331071-40331080 chr21:40331948-40331957 chr21:40331070-40331079
4	CTCF	chr21:40331460-40331610	AG10803	skin:	n/a	n/a
5	SRF	chr21:40330916-40331626	MCF-7	breast:	n/a	chr21:40331234-40331252 chr21:40331281-40331299
6	POLR2A	chr21:40331204-40332367	HepG2	liver:	n/a	n/a
7	POLR2A	chr21:40331362-40331638	MCF10A-Er-Src	breast:	n/a	n/a
8	MAX	chr21:40331262-40331818	NB4	blood:	n/a	n/a
9	POLR2A	chr21:40331215-40331862	HepG2	liver:	n/a	n/a
10	KAP1	chr21:40330862-40331776	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40282678..40285377-chr21:40330917..40333289,2	MCF-7	breast:
2	chr21:40280234..40282411-chr21:40330547..40333057,2	MCF-7	breast:
3	chr21:40330835..40334346-chr21:40336648..40339574,3	K562	blood:
4	chr21:40331496..40334558-chr21:40337329..40339575,3	MCF-7	breast:
5	chr21:40186991..40189987-chr21:40329579..40332415,2	K562	blood:
6	chr21:40208550..40210210-chr21:40331098..40333254,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205622	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10854393	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10854394	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10854395	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11088460	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs11088461	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs12165276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836793	1.00[ASN][1000 genomes]
rs2836794	1.00[ASN][1000 genomes]
rs60997307	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7278217	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7283257	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8126897	0.86[ASN][1000 genomes]
rs8129750	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8131869	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8133475	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs881558	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9980681	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9981682	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9982548	0.84[ASW][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs9982800	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9983903	1.00[ASN][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

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40326000-40331800	Enhancers	Stomach Mucosa	stomach
2	chr21:40326000-40332200	Enhancers	Fetal Lung	lung
3	chr21:40326200-40332800	Enhancers	Fetal Intestine Large	intestine
4	chr21:40326400-40332400	Enhancers	Fetal Intestine Small	intestine
5	chr21:40326800-40331800	Enhancers	Fetal Stomach	stomach
6	chr21:40326800-40331800	Enhancers	NHEK	skin
7	chr21:40326800-40332000	Enhancers	HMEC	breast
8	chr21:40327200-40332200	Enhancers	NHLF	lung
9	chr21:40327400-40332000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr21:40327400-40332000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr21:40327400-40332400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr21:40327600-40332400	Enhancers	Placenta	Placenta
13	chr21:40327800-40332000	Enhancers	Fetal Thymus	thymus
14	chr21:40328200-40332200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr21:40328400-40331800	Enhancers	Duodenum Mucosa	Duodenum
16	chr21:40328600-40332200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr21:40328800-40332000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr21:40329000-40332000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr21:40329000-40332400	Enhancers	NHDF-Ad	bronchial
20	chr21:40329000-40333200	Enhancers	Dnd41	blood
21	chr21:40329200-40331800	Enhancers	Osteobl	bone
22	chr21:40329400-40331800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr21:40329400-40332000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr21:40329400-40332200	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr21:40329400-40332200	Enhancers	K562	blood
26	chr21:40329400-40334200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr21:40329600-40332000	Enhancers	Thymus	Thymus
28	chr21:40329600-40332400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr21:40329800-40331800	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr21:40329800-40331800	Enhancers	Gastric	stomach
31	chr21:40329800-40332800	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr21:40330000-40331800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr21:40330000-40331800	Enhancers	Small Intestine	intestine
34	chr21:40330200-40332000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr21:40330200-40332200	Enhancers	Fetal Kidney	kidney
36	chr21:40330200-40332400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr21:40330400-40332000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr21:40330400-40332400	Enhancers	HSMMtube	muscle
39	chr21:40330400-40336400	Weak transcription	Brain Angular Gyrus	brain
40	chr21:40330600-40331800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr21:40330600-40331800	Enhancers	Muscle Satellite Cultured Cells	--
42	chr21:40330600-40332000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr21:40330800-40331800	Flanking Active TSS	Liver	Liver
44	chr21:40330800-40331800	Enhancers	Hela-S3	cervix
45	chr21:40330800-40331800	Enhancers	HSMM	muscle
46	chr21:40330800-40331800	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr21:40331000-40331800	Flanking Active TSS	HepG2	liver
48	chr21:40331000-40332000	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr21:40331200-40331800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr21:40331200-40331800	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links