Variant report

Variant	rs2609260
Chromosome Location	chr4:89836819-89836820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10031518	0.84[ASN][1000 genomes]
rs10470936	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs11722033	0.80[ASN][1000 genomes]
rs1246629	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1246631	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1246632	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1246634	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1246642	0.83[MEX][hapmap]
rs13110699	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1379932	0.81[CHD][hapmap]
rs1458551	0.94[MEX][hapmap];0.89[AMR][1000 genomes]
rs1563689	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1585258	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2446300	0.82[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2446301	0.81[CHB][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2446303	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2446304	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2464520	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464522	0.82[ASN][1000 genomes]
rs2464523	0.82[ASN][1000 genomes]
rs2464528	0.84[CHD][hapmap];0.94[MEX][hapmap];0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2609255	0.84[CHD][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes]
rs2609258	0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2609259	0.81[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2609261	0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2609262	0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2609264	0.84[CHD][hapmap];0.94[MEX][hapmap];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2609265	0.94[MEX][hapmap];0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2609279	0.82[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2609280	0.82[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2609282	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704570	0.86[AMR][1000 genomes]
rs2704581	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2704582	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2704583	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2704587	0.84[ASN][1000 genomes]
rs2704589	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs2704604	0.81[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2869952	0.86[AMR][1000 genomes]
rs6813090	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6815970	0.89[AMR][1000 genomes]
rs6838424	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs7673818	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7691363	0.80[ASN][1000 genomes]
rs9307058	0.81[ASN][1000 genomes]
rs9997652	0.81[AMR][1000 genomes];0.81[ASN][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	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv998651	chr4:89800245-89933445	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv537175	chr4:89800245-89933445	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv879532	chr4:89811195-89917135	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv879533	chr4:89832532-89917135	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2609260	HERC3	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89820000-89859200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:89825600-89878400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:89826000-89839600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:89826400-89838400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:89827200-89837400	Weak transcription	Fetal Lung	lung
6	chr4:89827200-89847000	Weak transcription	Placenta	Placenta
7	chr4:89827400-89847000	Weak transcription	Ovary	ovary
8	chr4:89828000-89847000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:89829200-89839400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:89833800-89841200	Weak transcription	Fetal Intestine Small	intestine
11	chr4:89836800-89842000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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