Variant report

Variant	rs10506188
Chromosome Location	chr12:41755304-41755305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:41754640..41756533-chr12:41757713..41760164,2	K562	blood:
2	chr12:41753701..41755841-chr12:41755916..41757984,2	MCF-7	breast:
3	chr12:41753620..41755968-chr12:41842392..41845001,2	K562	blood:

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1000147	0.96[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs10467086	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10506186	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10506187	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10506189	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10735991	0.99[EUR][1000 genomes]
rs10748300	0.94[CEU][hapmap];0.99[EUR][1000 genomes]
rs10748301	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10748302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785236	1.00[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs10785237	0.98[EUR][1000 genomes]
rs10785238	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10785239	0.98[EUR][1000 genomes]
rs10785240	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10785241	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10785242	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10785243	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10785244	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10785245	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10785247	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10785248	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10785249	0.99[EUR][1000 genomes]
rs10785250	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10785252	0.99[EUR][1000 genomes]
rs10785254	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10785255	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];1.00[EUR][1000 genomes]
rs10785256	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10785269	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10880038	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs10880039	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10880040	0.98[EUR][1000 genomes]
rs10880042	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10880043	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10880044	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10880046	0.97[EUR][1000 genomes]
rs10880047	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10880048	0.97[EUR][1000 genomes]
rs10880049	0.97[EUR][1000 genomes]
rs10880050	0.97[EUR][1000 genomes]
rs10880051	0.94[EUR][1000 genomes]
rs10880052	0.99[EUR][1000 genomes]
rs10880053	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10880055	0.99[EUR][1000 genomes]
rs10880056	1.00[EUR][1000 genomes]
rs10880057	0.99[EUR][1000 genomes]
rs10880058	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10880059	0.99[EUR][1000 genomes]
rs10880061	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10880062	1.00[EUR][1000 genomes]
rs10880081	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10880082	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10880086	0.80[CHB][hapmap]
rs10880087	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10880088	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11180837	0.97[EUR][1000 genomes]
rs11180838	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11180842	0.99[EUR][1000 genomes]
rs11180846	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs11180847	0.99[EUR][1000 genomes]
rs11180848	0.99[EUR][1000 genomes]
rs11180936	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11180943	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11180961	0.85[JPT][hapmap]
rs12315067	0.99[EUR][1000 genomes]
rs12368074	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12372586	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1317540	0.99[EUR][1000 genomes]
rs1317541	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1405550	0.99[EUR][1000 genomes]
rs1405551	0.99[EUR][1000 genomes]
rs1405557	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1465072	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs1609058	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1609059	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1609060	0.98[EUR][1000 genomes]
rs1609061	0.98[EUR][1000 genomes]
rs169564	1.00[JPT][hapmap]
rs17579291	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1918219	0.99[EUR][1000 genomes]
rs1918220	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1918222	0.99[EUR][1000 genomes]
rs1918223	0.98[EUR][1000 genomes]
rs1918225	0.99[EUR][1000 genomes]
rs1918228	0.99[EUR][1000 genomes]
rs1918236	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1918237	0.98[EUR][1000 genomes]
rs1918238	0.98[EUR][1000 genomes]
rs1949947	0.98[EUR][1000 genomes]
rs1949948	0.98[EUR][1000 genomes]
rs1949949	0.94[EUR][1000 genomes]
rs1949950	0.94[EUR][1000 genomes]
rs2141105	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2177974	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2204591	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2405910	0.99[EUR][1000 genomes]
rs2599254	0.82[JPT][hapmap]
rs2608709	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2730812	1.00[JPT][hapmap]
rs2730831	1.00[JPT][hapmap]
rs2730832	1.00[JPT][hapmap]
rs285551	1.00[JPT][hapmap]
rs285559	1.00[JPT][hapmap]
rs285588	1.00[JPT][hapmap]
rs285596	1.00[JPT][hapmap]
rs285597	1.00[JPT][hapmap]
rs287087	1.00[JPT][hapmap]
rs2897266	0.98[EUR][1000 genomes]
rs2897267	0.99[EUR][1000 genomes]
rs3110189	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4430580	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4768345	0.98[EUR][1000 genomes]
rs4768346	0.98[EUR][1000 genomes]
rs4768347	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4768348	0.95[CEU][hapmap];0.98[EUR][1000 genomes]
rs4768355	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7133806	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7138183	0.99[EUR][1000 genomes]
rs7298511	0.95[CEU][hapmap];0.99[EUR][1000 genomes]
rs7298953	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7299325	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7304306	0.97[EUR][1000 genomes]
rs7310743	0.99[EUR][1000 genomes]
rs7315905	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7959175	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7962343	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs941190	1.00[CEU][hapmap];0.99[EUR][1000 genomes]

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	nsv832383	chr12:41693298-41846934	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10506188	PDZRN4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41749600-41755400	Weak transcription	Brain Germinal Matrix	brain
2	chr12:41754600-41755800	Enhancers	Fetal Brain Male	brain
3	chr12:41755000-41759600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:41755200-41755600	Enhancers	Brain Substantia Nigra	brain
5	chr12:41755200-41756800	Enhancers	Colon Smooth Muscle	Colon

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