Variant report

Variant	rs11589817
Chromosome Location	chr1:212444738-212444739
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212441608..212446276-chr1:212456741..212460393,6	K562	blood:
2	chr1:212439869..212442717-chr1:212444447..212446810,3	K562	blood:
3	chr1:212441608..212446512-chr1:212456741..212460903,9	K562	blood:

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10494951	0.90[TSI][hapmap]
rs10863960	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10863961	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10863963	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11119899	0.94[ASN][1000 genomes]
rs11119919	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11119920	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11119924	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11119930	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11576437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579999	0.84[ASN][1000 genomes]
rs11580285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585215	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11587555	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11588867	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11590242	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs11590672	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12060029	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs12064553	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12066356	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12096035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12722832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12726409	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12727947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12728266	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12730098	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12734895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12736502	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12743785	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12745269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747025	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12756678	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1470390	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1493600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530451	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17721302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2120770	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap]
rs2297306	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2358448	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2358454	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs34212128	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34244392	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34447409	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34740542	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35872305	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55814152	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6661987	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6667199	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6676208	0.87[TSI][hapmap]
rs71646153	0.83[EUR][1000 genomes]
rs7518399	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs7521041	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7531219	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs968531	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs968532	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11589817	RP11-15I11.3	cis	lung	GTEx
rs11589817	RP11-15I11.3	cis	Thyroid	GTEx
rs11589817	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx
rs11589817	RP11-15I11.3	cis	Nerve Tibial	GTEx
rs11589817	KCNH1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212435200-212445600	Weak transcription	Right Atrium	heart
2	chr1:212435800-212444800	Weak transcription	Fetal Intestine Large	intestine
3	chr1:212442600-212446200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:212442800-212444800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:212442800-212445400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:212443400-212445600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr1:212443600-212445200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:212443600-212445600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:212444200-212445400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:212444400-212446400	Enhancers	Primary T cells from cord blood	blood
11	chr1:212444400-212446600	Enhancers	Fetal Intestine Small	intestine
12	chr1:212444600-212445000	Weak transcription	Pancreas	Pancrea
13	chr1:212444600-212446000	Enhancers	Stomach Mucosa	stomach
14	chr1:212444600-212446200	Enhancers	HepG2	liver

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