Variant report

Variant	rs12346640
Chromosome Location	chr9:117946614-117946615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10120799	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs10122188	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs10124924	0.88[EUR][1000 genomes]
rs10125919	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs10125923	0.88[EUR][1000 genomes]
rs10125938	0.88[EUR][1000 genomes]
rs10465131	0.81[EUR][1000 genomes]
rs10817709	0.88[CEU][hapmap]
rs10817719	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs10817720	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs10982518	0.88[CEU][hapmap]
rs10982519	0.88[CEU][hapmap]
rs10982578	0.86[EUR][1000 genomes]
rs10982580	0.82[EUR][1000 genomes]
rs10982583	0.81[EUR][1000 genomes]
rs10982586	0.81[EUR][1000 genomes]
rs10982588	0.83[EUR][1000 genomes]
rs10982589	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs10982590	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs10982591	0.81[EUR][1000 genomes]
rs10982592	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs10982596	0.91[EUR][1000 genomes]
rs10982597	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs10982600	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12115360	0.85[EUR][1000 genomes]
rs12115362	0.88[EUR][1000 genomes]
rs12339665	0.84[EUR][1000 genomes]
rs12344929	0.87[CEU][hapmap]
rs12345367	0.83[EUR][1000 genomes]
rs13289510	0.88[EUR][1000 genomes]
rs1335334	0.88[CEU][hapmap]
rs2274835	0.88[CEU][hapmap]
rs34459511	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35263530	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789871	0.88[CEU][hapmap]
rs4607691	0.88[EUR][1000 genomes]
rs60715510	0.86[EUR][1000 genomes]
rs6478140	0.81[EUR][1000 genomes]
rs6478141	0.81[EUR][1000 genomes]
rs6478142	0.81[EUR][1000 genomes]
rs7027851	0.81[EUR][1000 genomes]
rs7030384	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7048739	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs7357687	0.83[EUR][1000 genomes]
rs7357688	0.83[EUR][1000 genomes]
rs7847093	0.81[EUR][1000 genomes]
rs7851019	0.81[EUR][1000 genomes]
rs7851086	0.81[EUR][1000 genomes]
rs7851110	0.81[EUR][1000 genomes]
rs7851481	0.81[EUR][1000 genomes]
rs7862558	0.81[EUR][1000 genomes]
rs9299221	0.83[EUR][1000 genomes]
rs9886849	0.83[EUR][1000 genomes]
rs9886855	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv893769	chr9:117936903-117985886	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117930000-117964400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:117943200-117947000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr9:117944000-117947200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr9:117944400-117947000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:117944800-117947000	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:117945600-117947000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:117945600-117959400	Weak transcription	Fetal Kidney	kidney
8	chr9:117945800-117959600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:117946600-117947000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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