Variant report

Variant	rs17004592
Chromosome Location	chr21:45065012-45065013
allele	C/T
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:44936296..44939345-chr21:45062332..45065604,3	MCF-7	breast:
2	chr21:44589709..44591969-chr21:45063947..45066903,2	MCF-7	breast:
3	chr21:45040425..45043053-chr21:45064104..45066805,2	K562	blood:
4	chr21:44595798..44598770-chr21:45063265..45067849,4	MCF-7	breast:
5	chr21:44924498..44927329-chr21:45064955..45067005,2	MCF-7	breast:
6	chr21:44596809..44598374-chr21:45064063..45066950,2	K562	blood:
7	chr21:44845491..44848059-chr21:45064442..45068550,5	MCF-7	breast:
8	chr21:45031815..45032449-chr21:45065002..45065650,2	MCF-7	breast:
9	chr21:44752140..44754779-chr21:45064599..45066256,2	MCF-7	breast:
10	chr21:44934396..44939488-chr21:45063795..45068503,7	MCF-7	breast:
11	chr21:44920448..44924375-chr21:45064080..45067016,3	MCF-7	breast:
12	chr21:44844308..44847193-chr21:45063897..45069393,7	MCF-7	breast:
13	chr21:45031421..45032366-chr21:45064813..45066113,4	K562	blood:
14	chr21:45031379..45032049-chr21:45064870..45066020,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160202	Chromatin interaction
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10427514	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10483077	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs10483078	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11089090	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11908919	0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs11909195	0.83[AMR][1000 genomes]
rs11909530	0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs11909813	0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs11909916	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11911293	0.92[YRI][hapmap];0.91[AMR][1000 genomes]
rs11911735	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs11911856	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs12626631	0.85[YRI][hapmap]
rs17004507	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004581	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004585	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004586	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004587	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004589	0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004590	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004593	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004594	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004595	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004596	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28431406	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28782771	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28852206	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7510543	0.83[AMR][1000 genomes]
rs9917493	1.00[AFR][1000 genomes];1.00[AMR][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	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834106	chr21:44992387-45109489	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	15 gene(s)	inside rSNPs	diseases
3	nsv587700	chr21:45007956-45095200	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv913874	chr21:45041790-45191005	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45052200-45065200	Weak transcription	Primary T cells from cord blood	blood
2	chr21:45053200-45065200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr21:45058800-45065600	Weak transcription	Right Atrium	heart
4	chr21:45060400-45065200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr21:45060400-45065200	Weak transcription	Colonic Mucosa	Colon
6	chr21:45060400-45065200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr21:45060400-45065200	Weak transcription	Fetal Intestine Large	intestine
8	chr21:45060400-45065200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr21:45060400-45065200	Weak transcription	NHLF	lung
10	chr21:45060400-45078600	Weak transcription	Pancreas	Pancrea
11	chr21:45061400-45065600	Weak transcription	Stomach Mucosa	stomach
12	chr21:45063200-45065600	Enhancers	Fetal Brain Female	brain
13	chr21:45063400-45065200	Weak transcription	Fetal Intestine Small	intestine
14	chr21:45063400-45066200	Enhancers	Fetal Brain Male	brain
15	chr21:45063400-45066400	Weak transcription	Fetal Kidney	kidney
16	chr21:45063400-45066600	Enhancers	HSMM	muscle
17	chr21:45063800-45066600	Enhancers	NHEK	skin
18	chr21:45064000-45065600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr21:45064000-45066600	Enhancers	Fetal Lung	lung
20	chr21:45064200-45065200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr21:45064200-45065800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr21:45064200-45066200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr21:45064200-45066400	Flanking Active TSS	A549	lung
24	chr21:45064200-45066600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr21:45064200-45066600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr21:45064200-45066600	Enhancers	NH-A	brain
27	chr21:45064400-45065200	Weak transcription	Fetal Stomach	stomach
28	chr21:45064400-45065200	Enhancers	Hela-S3	cervix
29	chr21:45064400-45065400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr21:45064400-45065600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr21:45064400-45066000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr21:45064400-45066000	Flanking Active TSS	Osteobl	bone
33	chr21:45064400-45066600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr21:45064400-45066600	Enhancers	Brain Hippocampus Middle	brain
35	chr21:45064400-45066600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr21:45064400-45066600	Enhancers	NHDF-Ad	bronchial
37	chr21:45064400-45066800	Enhancers	HUVEC	blood vessel
38	chr21:45064400-45067000	Enhancers	HepG2	liver
39	chr21:45064600-45065200	Enhancers	Small Intestine	intestine
40	chr21:45064600-45065400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr21:45064600-45065400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr21:45064600-45065600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr21:45064600-45065600	Enhancers	GM12878-XiMat	blood
44	chr21:45064600-45065800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr21:45064600-45066600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr21:45064600-45066600	Enhancers	Placenta	Placenta
47	chr21:45064600-45066800	Enhancers	HMEC	breast
48	chr21:45064800-45065200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr21:45064800-45066600	Enhancers	HSMMtube	muscle
50	chr21:45065000-45065400	Enhancers	Sigmoid Colon	Sigmoid Colon

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