Variant report

Variant	rs4820997
Chromosome Location	chr22:32324140-32324141
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	22:32012966-32043914..22:32321495-32324143	GM12878	blood:
2	22:31803954-31807204..22:32321495-32324143	GM12878	blood:
3	chr22:32321616..32325715-chr22:32339030..32342356,3	MCF-7	breast:
4	22:32170492-32188129..22:32321495-32324143	GM12878	blood:
5	22:32228866-32235273..22:32321495-32324143	GM12878	blood:
6	chr22:32320601..32327336-chr22:32339153..32343531,7	K562	blood:
7	22:32162110-32166713..22:32321495-32324143	GM12878	blood:
8	22:32292186-32294405..22:32321495-32324143	GM12878	blood:
9	chr22:32324129..32327754-chr22:32332093..32337306,5	K562	blood:
10	22:31836635-31847259..22:32321495-32324143	GM12878	blood:
11	chr22:32323158..32326608-chr22:32339959..32342219,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000241878	Chromatin interaction
ENSG00000252909	Chromatin interaction
ENSG00000100150	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000128254	Chromatin interaction
ENSG00000128245	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11703587	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703779	0.87[CEU][hapmap];0.80[CHB][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16989609	0.81[LWK][hapmap];0.81[MKK][hapmap]
rs2015580	0.82[CEU][hapmap]
rs3213524	0.81[LWK][hapmap];0.82[YRI][hapmap]
rs3788436	0.81[LWK][hapmap];0.82[YRI][hapmap]
rs4820994	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs4820996	0.91[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4820998	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4820999	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749339	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753816	0.87[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753818	0.91[CEU][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753820	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5994449	0.81[JPT][hapmap]
rs5994451	0.91[CEU][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5998168	0.88[ASN][1000 genomes]
rs5998170	0.89[JPT][hapmap];0.82[YRI][hapmap]
rs5998172	0.89[JPT][hapmap]
rs5998176	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9619241	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4820997	EMID1	cis	parietal	SCAN
rs4820997	ZNRF3	cis	parietal	SCAN
rs4820997	C22orf31	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32302000-32324800	Weak transcription	Fetal Thymus	thymus
2	chr22:32304400-32339600	Weak transcription	Brain Germinal Matrix	brain
3	chr22:32315000-32324800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr22:32319000-32325200	Weak transcription	Brain Anterior Caudate	brain
5	chr22:32319600-32324800	Weak transcription	K562	blood
6	chr22:32319600-32338000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr22:32320000-32325000	Weak transcription	Brain Hippocampus Middle	brain
8	chr22:32320400-32324800	Weak transcription	Fetal Muscle Leg	muscle
9	chr22:32323000-32325000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:32323000-32325000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr22:32323000-32325000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr22:32323400-32328800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr22:32323600-32324800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr22:32323600-32324800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr22:32324000-32325000	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links