Variant report

Variant	rs11168355
Chromosome Location	chr12:48410978-48410979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48395740..48398491-chr12:48410326..48412487,2	MCF-7	breast:
2	chr12:48409071..48411163-chr12:48439800..48441969,2	MCF-7	breast:
3	chr12:48410357..48413530-chr12:48413703..48417962,3	K562	blood:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10082861	0.82[CHB][hapmap]
rs10875720	0.93[ASN][1000 genomes]
rs10875722	0.93[ASN][1000 genomes]
rs10875723	0.92[ASN][1000 genomes]
rs10875724	0.84[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875725	0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[ASN][1000 genomes]
rs10875730	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875731	0.90[ASN][1000 genomes]
rs10875732	0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10875745	0.88[GIH][hapmap]
rs10875746	0.92[GIH][hapmap]
rs10875750	1.00[GIH][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs10875772	0.82[YRI][hapmap]
rs11168357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168369	0.94[CHB][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11168371	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs11168374	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11168403	0.95[CHB][hapmap]
rs11168414	1.00[GIH][hapmap];0.85[LWK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs11168418	1.00[GIH][hapmap];0.85[TSI][hapmap]
rs11168420	1.00[GIH][hapmap];0.85[LWK][hapmap];0.85[TSI][hapmap]
rs11168421	0.84[GIH][hapmap]
rs11168425	0.93[GIH][hapmap]
rs11168427	1.00[GIH][hapmap];0.85[LWK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs11168433	1.00[GIH][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap]
rs12228854	0.82[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs12296244	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12297470	0.93[GIH][hapmap];0.85[JPT][hapmap]
rs12304476	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs12305182	0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12305511	0.88[GIH][hapmap];0.83[LWK][hapmap]
rs12306451	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap]
rs12310813	0.93[GIH][hapmap]
rs12310999	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17122666	0.83[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs1859445	0.96[GIH][hapmap]
rs1990028	0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2079295	0.93[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs2228500	1.00[GIH][hapmap];0.85[LWK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs2269933	0.89[GIH][hapmap]
rs2269935	0.84[GIH][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs2269936	0.95[CHB][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28459711	0.93[ASN][1000 genomes]
rs3782910	0.95[CHB][hapmap];0.82[YRI][hapmap]
rs3809322	1.00[YRI][hapmap]
rs4760609	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760610	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760622	0.88[GIH][hapmap]
rs4760676	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760681	0.96[GIH][hapmap];0.85[TSI][hapmap]
rs4760687	0.93[GIH][hapmap]
rs4760695	0.88[GIH][hapmap];0.83[LWK][hapmap];0.82[YRI][hapmap]
rs61918774	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs719008	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs725454	0.83[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs7299135	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs7299271	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs7299364	0.93[ASN][1000 genomes]
rs7964359	0.87[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs8804	1.00[GIH][hapmap];0.85[LWK][hapmap];0.85[TSI][hapmap]
rs886588	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs989144	0.95[CHB][hapmap];0.82[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11168355	RP1-228P16.1	cis	Artery Tibial	GTEx
rs11168355	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs11168355	SENP1	cis	parietal	SCAN
rs11168355	SENP1	cis	cerebellum	SCAN
rs11168355	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11168355	ASB8	cis	cerebellum	SCAN
rs11168355	PRKAG1	cis	parietal	SCAN
rs11168355	LOC255411	cis	cerebellum	SCAN
rs11168355	LMBR1L	cis	cerebellum	SCAN
rs11168355	RP1-228P16.1	cis	Thyroid	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48399400-48415000	Weak transcription	Right Atrium	heart
2	chr12:48407600-48411400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr12:48410200-48411400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48410200-48411600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48410200-48411600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:48410400-48411000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:48410400-48411200	Enhancers	HMEC	breast
8	chr12:48410400-48411400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:48410400-48411600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:48410600-48411000	Flanking Bivalent TSS/Enh	HepG2	liver
11	chr12:48410600-48412400	Enhancers	Fetal Intestine Large	intestine
12	chr12:48410600-48414800	Weak transcription	Hela-S3	cervix
13	chr12:48410800-48411000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:48410800-48412400	Enhancers	Fetal Intestine Small	intestine

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