Variant report

Variant	rs17016405
Chromosome Location	chr4:90878642-90878643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12233759	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61259703	0.85[ASN][1000 genomes]
rs62312664	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6828735	0.88[ASN][1000 genomes]
rs6830621	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv997700	chr4:90791866-90920021	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv830005	chr4:90799398-90963420	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1003903	chr4:90831805-90947922	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1011876	chr4:90851535-90952723	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv998230	chr4:90854555-90952723	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv999030	chr4:90859531-90952723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv432616	chr4:90862943-90952424	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv516189	chr4:90866819-90952424	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv594821	chr4:90871561-90962886	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv1793223	chr4:90876066-90880889	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17016405	MMRN1	cis	parietal	SCAN
rs17016405	C4orf36	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90876800-90882000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:90877800-90879200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr4:90878200-90878800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:90878200-90878800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr4:90878200-90878800	Enhancers	Fetal Lung	lung
6	chr4:90878200-90879000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr4:90878200-90879000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:90878200-90879200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr4:90878200-90879200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr4:90878200-90879200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr4:90878200-90879400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr4:90878400-90878800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:90878400-90878800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr4:90878400-90878800	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr4:90878600-90878800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:90878600-90878800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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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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