Variant report

Variant	rs274308
Chromosome Location	chr10:25246509-25246510
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:25245687..25248875-chr10:25261943..25265245,3	MCF-7	breast:
2	chr10:25245793..25250014-chr10:25304011..25307329,4	MCF-7	breast:
3	chr10:25245492..25247572-chr10:25252879..25256306,3	K562	blood:
4	chr10:25011700..25014356-chr10:25245305..25247951,2	K562	blood:
5	chr10:25242420..25244557-chr10:25246178..25248429,2	MCF-7	breast:
6	chr10:25245492..25247955-chr10:25250126..25255906,6	K562	blood:
7	chr10:25183976..25186724-chr10:25246241..25248282,2	K562	blood:
8	chr10:25246322..25248329-chr10:25271601..25273321,2	K562	blood:
9	chr10:25242028..25244551-chr10:25245660..25248271,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185875	Chromatin interaction
ENSG00000151023	Chromatin interaction
ENSG00000273107	Chromatin interaction
ENSG00000107863	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs185669	0.81[EUR][1000 genomes]
rs200730	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2478091	0.82[ASN][1000 genomes]
rs274288	0.81[ASN][1000 genomes]
rs274289	0.81[ASN][1000 genomes]
rs274299	0.81[ASN][1000 genomes]
rs274301	0.84[ASN][1000 genomes]
rs274302	0.87[ASN][1000 genomes]
rs274303	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs274304	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs274305	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs274306	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs274307	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs274309	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs274310	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs274311	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs274312	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs274313	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs274316	0.84[ASN][1000 genomes]
rs3000491	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053278	chr10:25140776-25269093	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25242200-25247800	Weak transcription	Aorta	Aorta
2	chr10:25242200-25247800	Weak transcription	Left Ventricle	heart
3	chr10:25242200-25248000	Weak transcription	Psoas Muscle	Psoas
4	chr10:25242400-25246600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr10:25242400-25246800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:25242400-25247400	Weak transcription	Ovary	ovary
7	chr10:25242400-25251400	Weak transcription	Liver	Liver
8	chr10:25242400-25252800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:25242600-25246800	Weak transcription	HUVEC	blood vessel
10	chr10:25242600-25247400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr10:25242600-25247600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr10:25242600-25249000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:25242800-25246600	Weak transcription	NHEK	skin
14	chr10:25242800-25247200	Weak transcription	Fetal Kidney	kidney
15	chr10:25242800-25247400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr10:25242800-25247600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr10:25242800-25247800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr10:25242800-25247800	Weak transcription	Right Atrium	heart
19	chr10:25242800-25251400	Weak transcription	Fetal Intestine Large	intestine
20	chr10:25242800-25251600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr10:25243000-25246600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr10:25243000-25246600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:25243000-25246800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr10:25243000-25246800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr10:25243000-25247000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr10:25243000-25247200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr10:25243000-25247200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr10:25243000-25247200	Weak transcription	Fetal Brain Female	brain
29	chr10:25243000-25247200	Weak transcription	Stomach Mucosa	stomach
30	chr10:25243000-25247600	Weak transcription	Fetal Brain Male	brain
31	chr10:25243000-25251400	Weak transcription	Fetal Intestine Small	intestine
32	chr10:25243200-25247600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr10:25243200-25247600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr10:25243200-25247600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr10:25243400-25246800	Weak transcription	Colon Smooth Muscle	Colon
36	chr10:25243400-25246800	Weak transcription	K562	blood
37	chr10:25243600-25247200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr10:25245400-25247000	Enhancers	Brain Anterior Caudate	brain
39	chr10:25245600-25246600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr10:25245600-25246800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr10:25245600-25246800	Enhancers	Brain Hippocampus Middle	brain
42	chr10:25245600-25247000	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr10:25245600-25247000	Enhancers	Fetal Muscle Leg	muscle
44	chr10:25245600-25247200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr10:25245600-25247200	Enhancers	Brain Cingulate Gyrus	brain
46	chr10:25245600-25247200	Enhancers	Fetal Lung	lung
47	chr10:25245600-25248400	Enhancers	HMEC	breast
48	chr10:25245600-25248600	Enhancers	Hela-S3	cervix
49	chr10:25245800-25246600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr10:25245800-25246600	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links