Variant report

Variant	rs17122565
Chromosome Location	chr12:48412410-48412411
allele	C/T
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	chr12:48411445..48413421-chr12:48418888..48421614,3	MCF-7	breast:
3	chr12:48406038..48410831-chr12:48411860..48418424,9	MCF-7	breast:
4	chr12:48391315..48400584-chr12:48411914..48418489,16	MCF-7	breast:
5	chr12:48407869..48410123-chr12:48411477..48413880,2	K562	blood:
6	chr12:48410357..48413530-chr12:48413703..48417962,3	K562	blood:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction
ENSG00000257955	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1018973	0.89[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs10492080	0.82[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs10783231	0.95[GIH][hapmap];0.95[JPT][hapmap]
rs10783232	0.87[GIH][hapmap];0.95[JPT][hapmap]
rs11168451	0.90[JPT][hapmap]
rs11168455	0.87[GIH][hapmap];0.91[JPT][hapmap]
rs11609399	0.95[JPT][hapmap]
rs11612578	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11613485	0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap]
rs12822085	0.92[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs1476608	0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs17122612	0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs17122651	0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs1968071	0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs3742074	0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs4075913	0.95[JPT][hapmap]
rs4141065	0.95[JPT][hapmap]
rs4760611	0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4760614	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4760616	0.89[EUR][1000 genomes]
rs4760617	0.91[EUR][1000 genomes]
rs4760620	0.90[GIH][hapmap];0.95[JPT][hapmap]
rs4760677	0.81[ASN][1000 genomes]
rs4760683	0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs4760685	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs4760692	0.95[JPT][hapmap]
rs4760698	0.87[GIH][hapmap];0.91[JPT][hapmap]
rs60629297	0.82[ASN][1000 genomes]
rs6580651	0.84[ASN][1000 genomes]
rs6580656	0.89[JPT][hapmap]
rs6580660	0.95[JPT][hapmap]
rs726354	0.82[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs72644841	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72644842	0.81[ASN][1000 genomes]
rs7296913	0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap]
rs7312326	0.95[JPT][hapmap]
rs7315258	0.90[GIH][hapmap];0.95[JPT][hapmap]
rs7485057	0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs757556	0.95[JPT][hapmap]
rs7959755	0.81[ASN][1000 genomes]
rs7963934	0.95[JPT][hapmap]
rs7969749	0.95[JPT][hapmap]
rs7971668	0.95[JPT][hapmap]
rs879242	0.95[JPT][hapmap]

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	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
2	esv2760677	chr12:48412410-48416967	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17122565	LASS5	cis	cerebellum	SCAN
rs17122565	H1T2	cis	multi-tissue	Pritchard
rs17122565	ZNF641	cis	Whole Blood	GTEx
rs17122565	MLL2	cis	cerebellum	SCAN
rs17122565	ASB8	cis	cerebellum	SCAN
rs17122565	ZNF641	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48399400-48415000	Weak transcription	Right Atrium	heart
2	chr12:48410600-48414800	Weak transcription	Hela-S3	cervix
3	chr12:48411400-48412600	Enhancers	HepG2	liver
4	chr12:48411600-48415000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48411600-48415200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:48412000-48415800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:48412200-48412800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr12:48412400-48412600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:48412400-48415000	Weak transcription	Fetal Intestine Large	intestine
10	chr12:48412400-48415000	Weak transcription	Fetal Intestine Small	intestine
11	chr12:48412400-48415000	Weak transcription	Rectal Mucosa Donor 31	rectum

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