Variant report

Variant	rs4623233
Chromosome Location	chr6:38414387-38414388
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10484927	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs12164032	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs12663177	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs16890641	0.84[CHB][hapmap]
rs16890743	0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs4711548	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4714166	0.83[ASN][1000 genomes]
rs73426885	0.80[ASN][1000 genomes]
rs9349080	0.87[ASN][1000 genomes]
rs9349085	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380744	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs9380746	0.90[CHB][hapmap]
rs9380749	0.93[ASN][1000 genomes]
rs9394496	0.89[CHB][hapmap];0.86[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1032358	chr6:38323745-38415855	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv602958	chr6:38362024-38446634	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1030889	chr6:38374812-38450432	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4623233	ZNF76	cis	cerebellum	SCAN
rs4623233	DEF6	cis	cerebellum	SCAN
rs4623233	ARG1	trans	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38396400-38449800	Weak transcription	Primary B cells from cord blood	blood
2	chr6:38405200-38420800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:38408200-38419200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:38412000-38415800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:38412000-38415800	Weak transcription	Psoas Muscle	Psoas
6	chr6:38412200-38445600	Weak transcription	Primary T cells from cord blood	blood
7	chr6:38412600-38419000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:38413000-38414400	Enhancers	Fetal Heart	heart
9	chr6:38413800-38414400	Enhancers	Liver	Liver
10	chr6:38413800-38414400	Enhancers	Brain Anterior Caudate	brain
11	chr6:38413800-38414400	Enhancers	Ovary	ovary
12	chr6:38413800-38414400	Enhancers	Right Atrium	heart
13	chr6:38413800-38414400	Enhancers	Small Intestine	intestine
14	chr6:38413800-38414800	Enhancers	Aorta	Aorta
15	chr6:38414000-38415000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr6:38414000-38438400	Weak transcription	Left Ventricle	heart

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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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