Variant report

Variant	rs1010764
Chromosome Location	chr5:147267730-147267731
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1153088	0.83[LWK][hapmap];0.80[YRI][hapmap]
rs11741382	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2250145	0.80[LWK][hapmap];0.80[YRI][hapmap]
rs3843496	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62378652	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3334831	chr5:147165950-147339765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv933308	chr5:147173804-147269006	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1028477	chr5:147255013-147416217	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1010764	SCGB3A2	cis	multi-tissue	Pritchard
rs1010764	CSF1R	cis	cerebellum	SCAN
rs1010764	UHRF2	trans	cerebellum	SCAN
rs1010764	GRPEL2	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147262600-147272600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:147262800-147272200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:147262800-147275600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:147266800-147268200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr5:147266800-147268200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr5:147266800-147268400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr5:147266800-147272200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:147267000-147268200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:147267000-147268200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:147267000-147268200	Enhancers	HUVEC	blood vessel
11	chr5:147267200-147268000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:147267200-147268000	Enhancers	NH-A	brain
13	chr5:147267200-147268400	Enhancers	HMEC	breast
14	chr5:147267400-147267800	Enhancers	Right Ventricle	heart
15	chr5:147267400-147268000	Enhancers	Hela-S3	cervix
16	chr5:147267400-147268200	Genic enhancers	Aorta	Aorta
17	chr5:147267400-147268200	Enhancers	NHEK	skin
18	chr5:147267600-147272800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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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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