Variant report

Variant	rs4912266
Chromosome Location	chr1:58071430-58071431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10889060	0.83[CHB][hapmap]
rs11808213	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12411177	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12562145	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524709	0.83[CHB][hapmap]
rs1534047	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17470462	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1829985	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2030719	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2140705	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61769601	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587787	0.83[CHB][hapmap]
rs6702155	0.83[CHB][hapmap]
rs72908555	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74077726	0.94[ASN][1000 genomes]
rs7528953	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531119	0.83[CHB][hapmap]
rs7532306	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1012555	chr1:57950355-58103389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv523574	chr1:58018103-58087789	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv871684	chr1:58021206-58096379	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv945968	chr1:58071136-58073409	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
8	esv3345240	chr1:58071339-58073462	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4912266	MYSM1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58065800-58071600	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr1:58066000-58077200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:58066000-58089000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:58066400-58089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:58066600-58074400	Weak transcription	Fetal Heart	heart
6	chr1:58069400-58072000	Enhancers	H9 Cell Line	embryonic stem cell
7	chr1:58069800-58071600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:58069800-58085400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:58070600-58072000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr1:58070800-58072000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:58071000-58071800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr1:58071000-58071800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr1:58071200-58071600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:58071200-58071600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr1:58071200-58072000	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr1:58071400-58071800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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Input of quick search could be:

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

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