Variant report

Variant	rs12152096
Chromosome Location	chr21:46496949-46496950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:46492353-46497285	IMR90	lung:	n/a	n/a
2	TBP	chr21:46496909-46497073	GM12878	blood:	n/a	n/a
3	CHD1	chr21:46493137-46497321	IMR90	lung:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65663723..65666241-chr21:46495274..46498090,2	K562	blood:
2	chr21:46495151..46497006-chr21:46906877..46909626,2	K562	blood:
3	chr21:46231513..46241255-chr21:46492035..46497390,26	K562	blood:
4	chr21:46348854..46378176-chr21:46489799..46500436,75	K562	blood:
5	chr21:46363747..46379047-chr21:46484156..46498795,67	K562	blood:
6	chr21:46492248..46501057-chr21:46545477..46562980,48	K562	blood:
7	chr21:46220974..46223825-chr21:46494380..46498218,5	MCF-7	breast:
8	chr21:46231904..46241990-chr21:46492035..46500735,28	K562	blood:
9	chr21:46492507..46498258-chr21:46706665..46711571,8	K562	blood:
10	chr21:46420509..46434696-chr21:46492036..46497081,20	K562	blood:
11	chr21:46387463..46395588-chr21:46492597..46498092,12	K562	blood:
12	chr21:46495879..46498410-chr21:46645680..46647627,2	K562	blood:
13	chr21:46492924..46497122-chr21:46547379..46551295,4	MCF-7	breast:
14	chr21:46495410..46497788-chr21:46536429..46538983,2	K562	blood:
15	chr21:46390745..46393297-chr21:46494598..46497120,2	MCF-7	breast:
16	chr21:46494846..46497722-chr21:46974690..46977147,2	K562	blood:
17	chr21:46494313..46497302-chr21:46514232..46516454,3	MCF-7	breast:
18	chr21:46398654..46417262-chr21:46491498..46498908,48	K562	blood:
19	chr21:46348334..46352514-chr21:46492914..46497675,5	K562	blood:
20	chr21:46495351..46497648-chr21:46516468..46519256,2	MCF-7	breast:
21	chr21:46491911..46497737-chr21:46547142..46552694,13	K562	blood:
22	chr21:46493097..46497182-chr21:46538705..46543454,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268856	TF binding region
SSR4P1	TF binding region
ENSG00000261706	Chromatin interaction
ENSG00000184787	Chromatin interaction
ENSG00000234880	Chromatin interaction
ENSG00000215447	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000184900	Chromatin interaction
ENSG00000268805	Chromatin interaction
ENSG00000272825	Chromatin interaction
ENSG00000273027	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000224930	Chromatin interaction
ENSG00000186866	Chromatin interaction
ENSG00000236519	Chromatin interaction
ENSG00000183250	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2003273	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2838764	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2838778	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2838787	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2838788	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8129315	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8132098	0.91[AFR][1000 genomes]
rs9983296	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9984236	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv834110	chr21:46316183-46505151	Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
3	esv3355416	chr21:46492024-46497122	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv3541	chr21:46496415-46536629	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46495400-46497000	Enhancers	Fetal Heart	heart
2	chr21:46495400-46497200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr21:46495600-46497000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr21:46495600-46497000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
5	chr21:46495600-46500200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr21:46495600-46501400	Weak transcription	Gastric	stomach
7	chr21:46495800-46497200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr21:46495800-46497200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr21:46495800-46497400	Weak transcription	A549	lung
10	chr21:46495800-46498400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr21:46495800-46498800	Weak transcription	NH-A	brain
12	chr21:46495800-46501400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr21:46495800-46502600	Weak transcription	Colonic Mucosa	Colon
14	chr21:46495800-46506000	Weak transcription	Pancreas	Pancrea
15	chr21:46496000-46497000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr21:46496000-46497000	Flanking Active TSS	Hela-S3	cervix
17	chr21:46496000-46497000	Flanking Active TSS	HMEC	breast
18	chr21:46496200-46497000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr21:46496200-46497000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr21:46496200-46497200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr21:46496200-46497400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr21:46496200-46498400	Weak transcription	Esophagus	oesophagus
23	chr21:46496200-46498800	Weak transcription	Right Ventricle	heart
24	chr21:46496200-46500000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr21:46496200-46501200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr21:46496200-46506600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr21:46496200-46511600	Weak transcription	Fetal Intestine Small	intestine
28	chr21:46496400-46497000	Enhancers	Primary B cells from peripheral blood	blood
29	chr21:46496400-46497000	Enhancers	Fetal Lung	lung
30	chr21:46496400-46497000	Enhancers	Fetal Muscle Leg	muscle
31	chr21:46496400-46497000	Enhancers	Rectal Smooth Muscle	rectum
32	chr21:46496400-46497000	Enhancers	HepG2	liver
33	chr21:46496400-46497200	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr21:46496400-46497200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr21:46496400-46498200	Weak transcription	Left Ventricle	heart
36	chr21:46496400-46498400	Weak transcription	Lung	lung
37	chr21:46496400-46498400	Weak transcription	Spleen	Spleen
38	chr21:46496400-46499800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr21:46496400-46501000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr21:46496400-46501000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr21:46496400-46501200	Weak transcription	Brain Anterior Caudate	brain
42	chr21:46496400-46501600	Weak transcription	Small Intestine	intestine
43	chr21:46496400-46509000	Enhancers	Primary T cells fromperipheralblood	blood
44	chr21:46496400-46509000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr21:46496400-46511400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr21:46496400-46511400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr21:46496400-46513000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr21:46496600-46497000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr21:46496600-46497000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr21:46496600-46497000	Enhancers	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links