Variant report

Variant	rs12103921
Chromosome Location	chr17:38354929-38354930
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38349831..38351927-chr17:38352533..38355067,3	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11078940	0.88[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs12941497	0.89[MEX][hapmap]
rs12944717	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16965666	0.85[JPT][hapmap]
rs16965687	0.88[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2280400	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2314338	0.82[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs28537537	0.88[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs34223321	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3744806	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4077125	0.88[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs45567834	0.99[ASN][1000 genomes]
rs4566234	0.88[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs4795424	0.89[MEX][hapmap]
rs55772196	0.98[ASN][1000 genomes]
rs55835834	0.87[ASN][1000 genomes]
rs55991953	0.98[ASN][1000 genomes]
rs56013073	0.99[ASN][1000 genomes]
rs56029626	0.90[ASN][1000 genomes]
rs59018914	0.87[ASN][1000 genomes]
rs59861136	0.90[ASN][1000 genomes]
rs61024420	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6503537	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6503539	0.88[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs67597966	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7211770	0.85[JPT][hapmap]
rs72836633	0.98[ASN][1000 genomes]
rs72836634	0.93[ASN][1000 genomes]
rs72836635	0.93[ASN][1000 genomes]
rs72836636	0.90[ASN][1000 genomes]
rs72836639	0.89[ASN][1000 genomes]
rs72836640	0.88[ASN][1000 genomes]
rs72836641	0.88[ASN][1000 genomes]
rs72836642	0.83[ASN][1000 genomes]
rs72836648	0.81[ASN][1000 genomes]
rs7359537	0.88[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7405635	0.84[ASW][hapmap];0.84[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8066144	0.88[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs8073925	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8082192	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs939347	0.84[MEX][hapmap]
rs9892404	0.81[ASN][1000 genomes]
rs9892946	0.88[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs9892973	0.99[ASN][1000 genomes]
rs9893520	0.88[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs9901109	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs9904021	0.88[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs9906409	0.81[ASN][1000 genomes]
rs9907683	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9908034	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9908257	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs9908354	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9911840	0.81[ASN][1000 genomes]
rs9912082	0.82[ASN][1000 genomes]
rs9916460	0.88[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs9916782	0.88[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv525796	chr17:38306365-38405037	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12103921	RAPGEFL1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38348400-38358200	Weak transcription	Adipose Nuclei	Adipose
2	chr17:38348400-38358400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr17:38348600-38358200	Weak transcription	HUVEC	blood vessel
4	chr17:38348600-38358200	Weak transcription	Osteobl	bone
5	chr17:38350000-38357400	Weak transcription	Placenta	Placenta
6	chr17:38350200-38359400	Weak transcription	Colonic Mucosa	Colon
7	chr17:38350400-38358000	Weak transcription	Liver	Liver
8	chr17:38350400-38358200	Weak transcription	Brain Hippocampus Middle	brain
9	chr17:38350400-38358200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr17:38350400-38358600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr17:38350800-38359400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr17:38350800-38359400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr17:38354600-38355000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr17:38354600-38355000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr17:38354600-38355000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr17:38354600-38355000	Active TSS	A549	lung
17	chr17:38354600-38355000	Flanking Active TSS	HepG2	liver
18	chr17:38354800-38358200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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