Variant report

Variant	rs61829734
Chromosome Location	chr10:3852542-3852543
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:3851273..3854029-chr10:3860569..3863821,3	MCF-7	breast:
2	chr10:3838224..3841156-chr10:3850289..3853010,2	MCF-7	breast:
3	chr10:3847609..3850397-chr10:3850957..3853100,3	MCF-7	breast:
4	chr10:3850418..3854705-chr10:3877438..3880204,3	K562	blood:
5	chr10:3851780..3854214-chr10:3872954..3875359,2	MCF-7	breast:
6	chr10:3851635..3854134-chr10:3920122..3921856,2	K562	blood:
7	chr10:3851733..3853926-chr10:3916076..3917752,2	MCF-7	breast:
8	chr10:3851673..3853403-chr10:3866040..3867619,2	MCF-7	breast:
9	chr10:3851797..3855219-chr10:3870977..3874184,3	MCF-7	breast:
10	chr10:3846663..3853057-chr10:3891702..3895719,6	MCF-7	breast:
11	chr10:3822110..3831216-chr10:3843525..3857606,41	MCF-7	breast:
12	chr10:3851668..3853539-chr10:3929673..3931804,2	MCF-7	breast:
13	chr10:3850046..3852996-chr10:3896621..3900254,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000067082	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10508267	0.96[ASN][1000 genomes]
rs10508268	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11252113	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12245875	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12248147	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12268277	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12761012	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17249633	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34180227	0.90[EUR][1000 genomes]
rs34414469	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61829729	0.84[ASN][1000 genomes]
rs61829733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043680	chr10:3551191-4038002	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv540450	chr10:3804336-3859639	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv540451	chr10:3804336-3868002	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv540456	chr10:3820854-3868002	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	n/a
5	nsv1045571	chr10:3839308-3874184	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
6	nsv540458	chr10:3839308-3874184	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:3844800-3854600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr10:3844800-3854600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr10:3845000-3854600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr10:3845000-3854600	Enhancers	Primary T cells from cord blood	blood
5	chr10:3845000-3854600	Enhancers	Fetal Thymus	thymus
6	chr10:3845400-3853200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:3846200-3852800	Enhancers	NHEK	skin
8	chr10:3846600-3852800	Enhancers	HMEC	breast
9	chr10:3846800-3854600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr10:3847400-3854600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr10:3847400-3854600	Enhancers	Fetal Intestine Large	intestine
12	chr10:3847600-3854600	Enhancers	Fetal Intestine Small	intestine
13	chr10:3847800-3852800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr10:3847800-3853600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr10:3848000-3853600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr10:3848000-3854600	Enhancers	Primary hematopoietic stem cells	blood
17	chr10:3848200-3855200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr10:3848600-3852800	Enhancers	Hela-S3	cervix
19	chr10:3848600-3854600	Enhancers	Stomach Mucosa	stomach
20	chr10:3848800-3852800	Enhancers	HUVEC	blood vessel
21	chr10:3848800-3853400	Weak transcription	Brain Substantia Nigra	brain
22	chr10:3849200-3853400	Weak transcription	Brain Anterior Caudate	brain
23	chr10:3849400-3853600	Enhancers	HSMM	muscle
24	chr10:3849400-3854400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr10:3849600-3853200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr10:3849600-3854600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr10:3849800-3853000	Weak transcription	Brain Hippocampus Middle	brain
28	chr10:3849800-3853600	Enhancers	NHDF-Ad	bronchial
29	chr10:3849800-3853800	Enhancers	NHLF	lung
30	chr10:3850000-3852800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr10:3850000-3852800	Weak transcription	Fetal Stomach	stomach
32	chr10:3850000-3853400	Enhancers	Adipose Nuclei	Adipose
33	chr10:3850200-3854600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr10:3850400-3852800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr10:3850600-3852800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr10:3850600-3852800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr10:3850600-3852800	Weak transcription	Fetal Brain Female	brain
38	chr10:3850600-3853200	Weak transcription	Brain Germinal Matrix	brain
39	chr10:3850800-3852600	Enhancers	Esophagus	oesophagus
40	chr10:3850800-3852800	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr10:3851200-3852600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr10:3851200-3852800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr10:3851200-3854600	Enhancers	Aorta	Aorta
44	chr10:3851400-3854000	Enhancers	Thymus	Thymus
45	chr10:3851400-3854400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr10:3851400-3856800	Enhancers	Fetal Heart	heart
47	chr10:3851600-3852800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr10:3851600-3853800	Flanking Active TSS	K562	blood
49	chr10:3851600-3854600	Enhancers	Primary B cells from peripheral blood	blood
50	chr10:3851600-3854600	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links