Variant report

Variant	rs3822955
Chromosome Location	chr6:119326375-119326376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:119319940..119322469-chr6:119324553..119327875,4	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1087451	0.97[ASN][1000 genomes]
rs1087452	0.97[ASN][1000 genomes]
rs12529321	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13209700	0.94[ASN][1000 genomes]
rs13214708	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1321837	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13219598	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1407204	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs17827619	0.94[ASN][1000 genomes]
rs2145568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs284921	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34455711	1.00[ASN][1000 genomes]
rs35375291	0.80[AMR][1000 genomes]
rs35795136	0.94[ASN][1000 genomes]
rs4245501	0.97[ASN][1000 genomes]
rs4946368	0.91[ASN][1000 genomes]
rs61108921	0.86[ASN][1000 genomes]
rs65685	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6915609	0.97[ASN][1000 genomes]
rs6915914	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[MEX][hapmap];0.86[ASN][1000 genomes]
rs706972	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs71559845	0.94[ASN][1000 genomes]
rs7743694	1.00[CHB][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.89[ASN][1000 genomes]
rs7746114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7766260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs794602	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs794609	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.97[ASN][1000 genomes]
rs794610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs794612	0.92[ASN][1000 genomes]
rs794613	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs794615	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs927288	0.94[ASN][1000 genomes]
rs9372516	0.91[ASN][1000 genomes]
rs9374750	1.00[JPT][hapmap]
rs9374758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9385056	1.00[JPT][hapmap]
rs9385064	1.00[CHB][hapmap];0.93[MEX][hapmap];0.89[ASN][1000 genomes]
rs9401108	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap]

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	nsv1030400	chr6:119320153-119433830	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3822955	TSPYL1	cis	cerebellum	SCAN
rs3822955	MCM9	cis	parietal	SCAN
rs3822955	MCM9	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119285800-119340000	Weak transcription	Fetal Brain Male	brain
2	chr6:119287200-119326600	Weak transcription	Fetal Brain Female	brain
3	chr6:119287400-119330000	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:119292400-119344000	Weak transcription	Brain Germinal Matrix	brain
5	chr6:119293200-119345400	Weak transcription	Lung	lung
6	chr6:119294200-119330800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:119300600-119344000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:119300800-119342600	Weak transcription	Brain Anterior Caudate	brain
9	chr6:119313000-119329800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:119314400-119364400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr6:119315400-119329800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:119315400-119330800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:119316600-119328800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:119318600-119344200	Weak transcription	Fetal Lung	lung
15	chr6:119319400-119330200	Weak transcription	Ovary	ovary
16	chr6:119319600-119333600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr6:119319800-119342600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr6:119320000-119327000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr6:119320400-119329200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:119321800-119329800	Weak transcription	Fetal Intestine Large	intestine
21	chr6:119322600-119337800	Weak transcription	Placenta	Placenta
22	chr6:119323600-119327200	Weak transcription	Aorta	Aorta
23	chr6:119324400-119331000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:119324400-119331000	Weak transcription	K562	blood
25	chr6:119324400-119333000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:119324800-119326600	Weak transcription	Adipose Nuclei	Adipose
27	chr6:119325200-119339800	Weak transcription	Primary T cells from cord blood	blood
28	chr6:119325400-119330600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:119325400-119349600	Weak transcription	Brain Angular Gyrus	brain
30	chr6:119325800-119327000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:119326000-119330200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:119326200-119326600	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links