Variant report

Variant	rs12355844
Chromosome Location	chr10:52835732-52835733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10822178	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10822190	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2339673	0.89[EUR][1000 genomes]
rs2339678	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2879523	0.88[EUR][1000 genomes]
rs2879547	0.89[EUR][1000 genomes]
rs4603249	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4935010	0.81[AMR][1000 genomes]
rs4935011	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4935214	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4935216	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4935220	0.84[EUR][1000 genomes]
rs4935221	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4935228	0.86[EUR][1000 genomes]
rs7904024	0.82[AMR][1000 genomes]
rs9414807	0.85[JPT][hapmap]
rs9414823	0.88[EUR][1000 genomes]
rs9415718	0.89[EUR][1000 genomes]
rs9415721	0.88[EUR][1000 genomes]
rs9415730	0.86[EUR][1000 genomes]
rs957717	0.81[EUR][1000 genomes]
rs987633	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[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	nsv831873	chr10:52710610-52899540	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv895394	chr10:52793177-52866503	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1036645	chr10:52804961-53159076	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52832800-52837400	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr10:52832800-52840000	Active TSS	Aorta	Aorta
3	chr10:52833000-52835800	Active TSS	Fetal Kidney	kidney
4	chr10:52833000-52836200	Active TSS	Psoas Muscle	Psoas
5	chr10:52833000-52836400	Active TSS	Right Ventricle	heart
6	chr10:52833000-52837000	Active TSS	Right Atrium	heart
7	chr10:52833000-52837600	Active TSS	Colon Smooth Muscle	Colon
8	chr10:52833200-52835800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:52833200-52835800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:52833200-52836000	Active TSS	H9 Cell Line	embryonic stem cell
11	chr10:52833200-52836400	Active TSS	Ovary	ovary
12	chr10:52833200-52836600	Active TSS	Rectal Smooth Muscle	rectum
13	chr10:52833200-52837600	Active TSS	NHLF	lung
14	chr10:52833400-52835800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr10:52833400-52836600	Active TSS	Brain Anterior Caudate	brain
16	chr10:52833600-52836400	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr10:52833600-52836400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
18	chr10:52833600-52836600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
19	chr10:52833600-52837200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr10:52833800-52836000	Active TSS	Brain Angular Gyrus	brain
21	chr10:52833800-52836400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:52833800-52837600	Active TSS	Stomach Smooth Muscle	stomach
23	chr10:52834200-52835800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr10:52834400-52835800	Active TSS	Fetal Brain Male	brain
25	chr10:52834400-52836200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
26	chr10:52834600-52836200	Active TSS	Fetal Brain Female	brain
27	chr10:52834800-52835800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
28	chr10:52834800-52836200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
29	chr10:52834800-52836600	Active TSS	Fetal Muscle Trunk	muscle
30	chr10:52834800-52837000	Active TSS	Fetal Stomach	stomach
31	chr10:52834800-52842800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr10:52835000-52835800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
33	chr10:52835000-52835800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr10:52835000-52836000	Bivalent/Poised TSS	Adipose Nuclei	Adipose
35	chr10:52835000-52836000	Active TSS	Brain Germinal Matrix	brain
36	chr10:52835200-52835800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr10:52835200-52836000	Enhancers	Fetal Lung	lung
38	chr10:52835200-52836200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr10:52835200-52836200	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr10:52835200-52837000	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr10:52835200-52837600	Active TSS	Fetal Muscle Leg	muscle
42	chr10:52835400-52835800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr10:52835400-52835800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
44	chr10:52835400-52835800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr10:52835400-52835800	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr10:52835400-52836400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr10:52835400-52836400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr10:52835400-52836400	Flanking Active TSS	NHDF-Ad	bronchial
49	chr10:52835400-52837600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr10:52835600-52835800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links