Variant report

Variant	rs9625600
Chromosome Location	chr22:29244395-29244396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC117-1	chr22:29244379-29244547	ENSG00000226471.2

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10154819	0.81[ASN][1000 genomes]
rs10427628	0.83[EUR][1000 genomes]
rs12170231	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1222	0.91[CEU][hapmap]
rs13053879	0.86[AFR][1000 genomes]
rs13056243	0.83[CEU][hapmap]
rs13058031	0.91[CEU][hapmap];0.86[AFR][1000 genomes]
rs13058460	0.93[ASN][1000 genomes]
rs16986825	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs16986838	1.00[YRI][hapmap]
rs16986864	0.83[CEU][hapmap]
rs17514713	1.00[YRI][hapmap]
rs2236141	0.83[CEU][hapmap]
rs2267131	0.91[CEU][hapmap]
rs2301428	0.91[CEU][hapmap]
rs2347448	0.86[AFR][1000 genomes]
rs34206997	0.86[AFR][1000 genomes]
rs35050306	0.86[AFR][1000 genomes]
rs35814864	0.86[AFR][1000 genomes]
rs4055	0.83[CEU][hapmap]
rs5752803	0.91[CEU][hapmap]
rs5752808	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5752810	1.00[CEU][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5752811	0.91[CEU][hapmap]
rs5752814	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752815	1.00[CEU][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5752816	0.86[AFR][1000 genomes]
rs5762767	0.91[CEU][hapmap]
rs5762780	0.91[CEU][hapmap]
rs5762814	0.91[CEU][hapmap]
rs5762816	0.91[CEU][hapmap]
rs5762826	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5762829	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5762835	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5762838	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5762839	1.00[CEU][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5762848	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5762852	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762857	0.86[AFR][1000 genomes]
rs5762858	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5762879	0.87[JPT][hapmap]
rs59203761	0.86[AFR][1000 genomes]
rs59224170	0.86[AFR][1000 genomes]
rs5997409	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6005917	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60468718	0.86[AFR][1000 genomes]
rs73170679	0.86[AFR][1000 genomes]
rs739196	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs9625591	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625595	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9625600	XBP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29226000-29248800	Weak transcription	Primary T cells from cord blood	blood
2	chr22:29234000-29251600	Weak transcription	Fetal Lung	lung
3	chr22:29243200-29245200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr22:29243200-29249800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr22:29243800-29244800	ZNF genes & repeats	Fetal Intestine Small	intestine

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