Variant report

Variant	rs12066356
Chromosome Location	chr1:212437720-212437721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212433329..212435940-chr1:212436148..212437997,2	K562	blood:
2	chr1:212432987..212434829-chr1:212436497..212438053,2	K562	blood:
3	chr1:212406214..212407731-chr1:212435193..212437929,2	K562	blood:
4	chr1:212428875..212432292-chr1:212434801..212437724,6	K562	blood:
5	chr1:212427899..212432292-chr1:212432529..212438731,7	K562	blood:
6	chr1:212404851..212407731-chr1:212434475..212437929,3	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10863960	0.96[ASN][1000 genomes]
rs10863961	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10863963	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11119899	0.96[ASN][1000 genomes]
rs11119919	1.00[JPT][hapmap]
rs11119920	1.00[JPT][hapmap]
rs11119924	0.88[CHB][hapmap]
rs11119930	0.88[CHB][hapmap]
rs11576437	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11579999	0.86[ASN][1000 genomes]
rs11580285	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11585215	0.88[ASN][1000 genomes]
rs11587555	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11588867	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11589817	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11590242	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12060029	0.88[CHB][hapmap]
rs12064553	0.86[ASN][1000 genomes]
rs12096035	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12722832	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12726409	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12727947	0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12728266	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12730098	0.98[ASN][1000 genomes]
rs12734895	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12736502	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12743785	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12745269	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12747025	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12756678	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12759994	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1470390	1.00[JPT][hapmap]
rs1493600	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1530451	0.94[ASN][1000 genomes]
rs17721302	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2120770	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2358448	0.88[ASN][1000 genomes]
rs2358454	1.00[JPT][hapmap]
rs34212128	0.98[ASN][1000 genomes]
rs34244392	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34447409	0.88[ASN][1000 genomes]
rs34740542	0.94[ASN][1000 genomes]
rs35872305	0.94[ASN][1000 genomes]
rs55814152	0.88[ASN][1000 genomes]
rs6661987	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6667199	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7513529	0.82[AFR][1000 genomes]
rs7518399	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7521041	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527863	0.82[AFR][1000 genomes]
rs7531219	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968531	0.88[ASN][1000 genomes]
rs968532	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	esv2461437	chr1:212436159-212437760	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12066356	RP11-15I11.3	cis	lung	GTEx
rs12066356	RP11-15I11.3	cis	Thyroid	GTEx
rs12066356	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212435200-212445600	Weak transcription	Right Atrium	heart
2	chr1:212435400-212444600	Weak transcription	Stomach Mucosa	stomach
3	chr1:212435600-212444400	Weak transcription	Fetal Intestine Small	intestine
4	chr1:212435800-212444800	Weak transcription	Fetal Intestine Large	intestine
5	chr1:212436000-212442600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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