Variant report

Variant	rs568401
Chromosome Location	chr10:97362091-97362092
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10509688	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs12414244	0.81[ASN][1000 genomes]
rs12414904	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs1270505	0.81[JPT][hapmap]
rs12768006	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs12769303	0.86[ASN][1000 genomes]
rs12773566	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs1933164	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs2485642	0.86[ASN][1000 genomes]
rs34297443	0.81[ASN][1000 genomes]
rs34826684	0.82[ASN][1000 genomes]
rs476392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483920	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs4918949	0.83[ASN][1000 genomes]
rs561156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs568401	TCTN3	cis	brain	BrainEAC
rs568401	TCTN3	cis	hippocampus	BrainEAC

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97335200-97373400	Weak transcription	Psoas Muscle	Psoas
2	chr10:97359400-97364600	Weak transcription	Placenta	Placenta
3	chr10:97360000-97364000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr10:97360200-97364400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr10:97360200-97364600	Weak transcription	GM12878-XiMat	blood
6	chr10:97360400-97364400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr10:97360400-97364600	Enhancers	HepG2	liver
8	chr10:97360600-97363200	Weak transcription	Right Ventricle	heart
9	chr10:97360600-97364000	Weak transcription	Right Atrium	heart
10	chr10:97360800-97362600	Enhancers	Fetal Intestine Large	intestine
11	chr10:97360800-97364400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr10:97360800-97364400	Weak transcription	Fetal Brain Female	brain
13	chr10:97360800-97364800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:97360800-97365000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr10:97360800-97365000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr10:97360800-97366200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr10:97361000-97363800	Weak transcription	Fetal Stomach	stomach
18	chr10:97361000-97364600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr10:97361000-97364600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:97361000-97364800	Weak transcription	Stomach Mucosa	stomach
21	chr10:97361000-97365000	Weak transcription	Adipose Nuclei	Adipose
22	chr10:97361000-97365000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr10:97361000-97365000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr10:97361000-97365200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr10:97361000-97366000	Weak transcription	Hela-S3	cervix
26	chr10:97361000-97366400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr10:97361000-97366800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr10:97361000-97367600	Weak transcription	Fetal Kidney	kidney
29	chr10:97361000-97368200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr10:97361000-97368400	Weak transcription	Brain Hippocampus Middle	brain
31	chr10:97361200-97363200	Weak transcription	Fetal Muscle Leg	muscle
32	chr10:97361200-97364200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr10:97361200-97364800	Weak transcription	Brain Anterior Caudate	brain
34	chr10:97361400-97363200	Weak transcription	HSMMtube	muscle
35	chr10:97361400-97363800	Weak transcription	Colon Smooth Muscle	Colon
36	chr10:97361400-97364000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr10:97361400-97364200	Weak transcription	Fetal Heart	heart
38	chr10:97361400-97364400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr10:97361400-97364400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr10:97361400-97364400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr10:97361400-97364600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr10:97361400-97365200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr10:97361400-97365800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr10:97361400-97366600	Weak transcription	K562	blood
45	chr10:97361600-97362400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr10:97361600-97364000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr10:97361600-97364800	Weak transcription	Osteobl	bone
48	chr10:97361600-97365000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr10:97361600-97367800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr10:97361800-97362600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links