Variant report

Variant	rs6539231
Chromosome Location	chr12:106211250-106211251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10507199	0.86[ASN][1000 genomes]
rs10732669	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10732670	0.88[ASN][1000 genomes]
rs10735409	0.88[ASN][1000 genomes]
rs10735410	0.95[ASN][1000 genomes]
rs10735411	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10735412	0.89[ASN][1000 genomes]
rs10735413	0.89[ASN][1000 genomes]
rs10746050	0.89[ASN][1000 genomes]
rs10778440	0.85[ASN][1000 genomes]
rs10778441	0.88[ASN][1000 genomes]
rs10778442	0.88[ASN][1000 genomes]
rs10778446	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10778447	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10778448	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861505	0.86[ASN][1000 genomes]
rs10861511	0.80[ASN][1000 genomes]
rs10861512	0.85[ASN][1000 genomes]
rs10861513	0.84[ASN][1000 genomes]
rs10861514	0.92[ASN][1000 genomes]
rs10861515	0.92[ASN][1000 genomes]
rs10861517	0.89[ASN][1000 genomes]
rs11112724	0.86[ASN][1000 genomes]
rs11112729	0.88[ASN][1000 genomes]
rs11112730	0.86[ASN][1000 genomes]
rs11112731	0.85[ASN][1000 genomes]
rs11112733	0.88[ASN][1000 genomes]
rs11112736	0.85[ASN][1000 genomes]
rs11112737	0.87[ASN][1000 genomes]
rs11112739	0.92[ASN][1000 genomes]
rs11112747	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11833529	0.86[ASN][1000 genomes]
rs12305658	0.86[ASN][1000 genomes]
rs12314159	0.92[ASN][1000 genomes]
rs12370329	0.86[ASN][1000 genomes]
rs1421445	0.92[ASN][1000 genomes]
rs1421446	0.92[ASN][1000 genomes]
rs1421447	0.97[ASN][1000 genomes]
rs1477238	0.92[ASN][1000 genomes]
rs1477239	0.92[ASN][1000 genomes]
rs1477240	0.92[ASN][1000 genomes]
rs1477242	0.92[ASN][1000 genomes]
rs1549103	0.88[ASN][1000 genomes]
rs2052428	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2111975	0.95[ASN][1000 genomes]
rs2111976	0.90[ASN][1000 genomes]
rs2374538	0.92[ASN][1000 genomes]
rs2888869	0.86[ASN][1000 genomes]
rs4270016	0.89[ASN][1000 genomes]
rs4337138	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4430602	0.92[ASN][1000 genomes]
rs4438139	0.88[ASN][1000 genomes]
rs4499093	0.86[ASN][1000 genomes]
rs4509865	0.88[ASN][1000 genomes]
rs4509866	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4516058	0.92[ASN][1000 genomes]
rs4600310	0.86[ASN][1000 genomes]
rs4609683	0.82[ASN][1000 genomes]
rs4609684	0.86[ASN][1000 genomes]
rs4964160	0.92[ASN][1000 genomes]
rs4964161	0.92[ASN][1000 genomes]
rs4964409	0.86[ASN][1000 genomes]
rs4964410	0.88[ASN][1000 genomes]
rs4964411	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4964413	0.88[ASN][1000 genomes]
rs4964414	0.85[ASN][1000 genomes]
rs4964415	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964416	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6539230	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7302776	0.91[ASN][1000 genomes]
rs7303862	0.83[ASN][1000 genomes]
rs7307825	0.91[ASN][1000 genomes]
rs7307959	0.89[ASN][1000 genomes]
rs7309925	0.91[ASN][1000 genomes]
rs7311274	0.91[ASN][1000 genomes]
rs7313258	0.86[ASN][1000 genomes]
rs7313292	0.86[ASN][1000 genomes]
rs750207	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs750208	0.92[ASN][1000 genomes]
rs7954139	0.92[ASN][1000 genomes]
rs7954308	0.92[ASN][1000 genomes]
rs7954604	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7956555	0.86[ASN][1000 genomes]
rs7964548	0.87[ASN][1000 genomes]
rs7968050	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7968132	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7970318	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7979193	0.92[ASN][1000 genomes]
rs7979632	0.92[ASN][1000 genomes]
rs878612	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9634186	0.88[ASN][1000 genomes]
rs9634187	0.86[ASN][1000 genomes]
rs9634188	0.86[ASN][1000 genomes]
rs9634189	0.88[ASN][1000 genomes]
rs9634227	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9634228	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9634229	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039068	chr12:105935786-106211250	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1047810	chr12:106067049-106246582	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1040261	chr12:106068992-106246582	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv832508	chr12:106198797-106409112	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6539231	PWP1	cis	parietal	SCAN
rs6539231	CCDC53	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106200200-106212400	Weak transcription	Left Ventricle	heart
2	chr12:106207000-106214000	Weak transcription	Right Atrium	heart
3	chr12:106207000-106214400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:106207400-106212800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:106207400-106214000	Weak transcription	Aorta	Aorta
6	chr12:106207400-106215400	Weak transcription	Fetal Stomach	stomach
7	chr12:106207400-106216000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:106208200-106211800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:106208200-106212600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:106208200-106215600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:106208800-106212000	Weak transcription	HSMMtube	muscle
12	chr12:106208800-106212400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:106209000-106214000	Weak transcription	Right Ventricle	heart
14	chr12:106209000-106214600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:106209000-106214600	Weak transcription	Fetal Thymus	thymus
16	chr12:106211000-106212400	Weak transcription	Psoas Muscle	Psoas

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