Variant report

Variant	rs322246
Chromosome Location	chr7:136960167-136960168
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10264510	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17169022	0.89[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs188915	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs322245	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72611540	0.82[ASN][1000 genomes]
rs72611541	0.82[ASN][1000 genomes]
rs72611542	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029192	chr7:136433278-137147566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831149	chr7:136831665-137006468	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv889238	chr7:136915059-136989606	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv889239	chr7:136923730-136994013	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs322246	CNOT4	cis	parietal	SCAN
rs322246	NUP205	cis	cerebellum	SCAN
rs322246	C7orf49	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:136938200-136980600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:136949000-136960800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:136952200-136960400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr7:136952200-136971000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:136952600-136960400	Weak transcription	Brain Substantia Nigra	brain
6	chr7:136957200-136960800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:136959800-136960800	Enhancers	Brain Angular Gyrus	brain
8	chr7:136959800-136961000	Enhancers	Brain Cingulate Gyrus	brain
9	chr7:136960000-136960200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:136960000-136960400	Weak transcription	Brain Hippocampus Middle	brain
11	chr7:136960000-136960800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr7:136960000-136961000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:136960000-136961000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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