Variant report

Variant	rs13009906
Chromosome Location	chr2:55739434-55739435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55495971..55497708-chr2:55737888..55740106,2	MCF-7	breast:
2	chr2:55738996..55741436-chr2:55745150..55747793,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163001	Chromatin interaction
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1013138	0.85[ASW][hapmap];0.82[JPT][hapmap]
rs12617627	0.93[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12618859	0.93[ASW][hapmap];0.83[JPT][hapmap];0.84[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap]
rs12619903	0.81[CEU][hapmap];0.92[YRI][hapmap]
rs12986444	0.83[AFR][1000 genomes]
rs12986587	0.85[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs12992408	0.92[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12992827	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs12993624	0.93[ASW][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs12993642	0.82[ASN][1000 genomes]
rs12998664	0.84[JPT][hapmap]
rs12998780	0.89[JPT][hapmap]
rs12998925	0.81[EUR][1000 genomes]
rs12999506	0.82[AFR][1000 genomes]
rs12999680	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12999966	0.81[CEU][hapmap];0.92[YRI][hapmap]
rs13001425	0.80[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.87[YRI][hapmap]
rs13005678	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13006502	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13009239	0.87[ASN][1000 genomes]
rs13009447	0.89[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]
rs13010217	0.93[ASW][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs13014898	0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13015018	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13015030	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13015744	0.89[JPT][hapmap]
rs13021958	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13025331	0.93[ASW][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs13027095	0.81[AFR][1000 genomes]
rs13027853	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13032503	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1318672	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17737233	0.84[JPT][hapmap]
rs1822513	0.85[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.87[YRI][hapmap]
rs2291336	0.84[JPT][hapmap]
rs34013926	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs34143512	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs34679603	0.80[ASN][1000 genomes]
rs35189503	0.80[ASN][1000 genomes]
rs3791654	0.89[JPT][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap]
rs3828238	0.85[ASW][hapmap];0.84[JPT][hapmap]
rs4312532	0.85[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs4322879	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5012561	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56122729	0.83[ASN][1000 genomes]
rs66545054	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6737995	0.93[ASW][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs6753530	0.84[JPT][hapmap]
rs6757006	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7575170	0.93[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.92[YRI][hapmap]
rs8080	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13009906	CCDC104	cis	parietal	SCAN
rs13009906	PNPT1	cis	cerebellum	SCAN
rs13009906	SMEK2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55739000-55741200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:55739000-55745600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:55739000-55745800	Weak transcription	Brain Angular Gyrus	brain
4	chr2:55739000-55745800	Weak transcription	Thymus	Thymus
5	chr2:55739000-55745800	Weak transcription	NHEK	skin

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