Variant report

Variant	rs9609389
Chromosome Location	chr22:32335416-32335417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:32333714..32338666-chr22:32338808..32341895,4	MCF-7	breast:
2	22:32284948-32287956..22:32334260-32338420	K562	blood:
3	chr22:32329388..32335571-chr22:32336708..32343906,17	K562	blood:

Variant related genes	Relation type
ENSG00000128245	Chromatin interaction
ENSG00000227813	Chromatin interaction
ENSG00000128254	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12159340	1.00[YRI][hapmap]
rs12167681	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs130256	0.93[CEU][hapmap]
rs130257	1.00[CEU][hapmap]
rs130264	0.93[CEU][hapmap]
rs130405	0.93[CEU][hapmap]
rs3761432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3827334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6518758	0.93[CEU][hapmap];0.96[MKK][hapmap]
rs7290696	1.00[ASW][hapmap]
rs7291050	1.00[ASW][hapmap]
rs738181	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[MKK][hapmap]
rs933226	0.93[CEU][hapmap]
rs9606893	0.93[CEU][hapmap]
rs9606907	0.80[CEU][hapmap]
rs9606908	0.80[CEU][hapmap]
rs9609390	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609409	0.93[CEU][hapmap]
rs9609427	0.80[CEU][hapmap]
rs9621371	1.00[ASW][hapmap]
rs9621386	0.80[CEU][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	nsv428046	chr22:32316302-32356963	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9609389	TUG1	cis	cerebellum	SCAN
rs9609389	RFPL1	cis	cerebellum	SCAN
rs9609389	CCDC117	cis	cerebellum	SCAN
rs9609389	LIF	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32304400-32339600	Weak transcription	Brain Germinal Matrix	brain
2	chr22:32319600-32338000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr22:32325200-32338800	Weak transcription	Fetal Thymus	thymus
4	chr22:32326000-32339600	Weak transcription	Fetal Lung	lung
5	chr22:32326400-32339200	Weak transcription	Fetal Stomach	stomach
6	chr22:32329200-32339600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr22:32330400-32339400	Weak transcription	Pancreas	Pancrea
8	chr22:32331200-32339600	Weak transcription	Brain Substantia Nigra	brain
9	chr22:32332200-32339600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr22:32332400-32339400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr22:32332400-32339600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:32332600-32335600	Enhancers	Fetal Brain Male	brain
13	chr22:32332600-32339400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr22:32332800-32339400	Weak transcription	Brain Hippocampus Middle	brain
15	chr22:32332800-32339400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr22:32332800-32339600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr22:32333000-32339600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr22:32333200-32338200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr22:32333400-32338600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr22:32333400-32339600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr22:32334000-32339400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr22:32334200-32339400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr22:32334200-32339400	Weak transcription	Fetal Heart	heart
24	chr22:32334600-32335600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr22:32334600-32339400	Weak transcription	Fetal Muscle Leg	muscle
26	chr22:32334800-32336800	Weak transcription	K562	blood
27	chr22:32334800-32339400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr22:32334800-32339400	Weak transcription	Fetal Brain Female	brain
29	chr22:32335400-32335600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr22:32335400-32335600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr22:32335400-32335600	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links