Variant report

Variant	rs1396880
Chromosome Location	chr11:34870552-34870553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:34831080..34832844-chr11:34868501..34870661,2	K562	blood:
2	chr11:34865938..34868708-chr11:34870452..34873276,2	K562	blood:
3	chr11:34863977..34866462-chr11:34870377..34873238,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1117051	0.81[JPT][hapmap]
rs1396881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509662	0.82[ASN][1000 genomes]
rs1549789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549791	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1553757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553758	0.89[ASN][1000 genomes]
rs1553759	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1553760	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1553761	0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1553762	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1828298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858166	0.89[ASN][1000 genomes]
rs1960524	0.82[JPT][hapmap]
rs1991648	0.82[JPT][hapmap]
rs2031686	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2033355	0.82[ASN][1000 genomes]
rs2116085	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2163374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163375	0.80[ASN][1000 genomes]
rs2421743	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2915177	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2915178	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2915179	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915180	0.89[ASN][1000 genomes]
rs2915198	0.82[JPT][hapmap]
rs2915214	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2915217	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2915225	0.82[JPT][hapmap]
rs2915237	0.80[ASN][1000 genomes]
rs2915238	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2941040	0.92[ASN][1000 genomes]
rs2941041	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2941042	0.89[ASN][1000 genomes]
rs2941043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2941044	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2941045	0.85[ASN][1000 genomes]
rs2941054	0.86[ASN][1000 genomes]
rs2941055	0.85[ASN][1000 genomes]
rs2941056	0.89[ASN][1000 genomes]
rs2941057	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2941058	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2941059	0.82[ASN][1000 genomes]
rs2941060	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2941061	0.86[ASN][1000 genomes]
rs2956074	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2956076	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956077	0.82[JPT][hapmap]
rs2956078	0.90[ASN][1000 genomes]
rs2956079	0.80[ASN][1000 genomes]
rs2956080	0.86[ASN][1000 genomes]
rs2956086	0.86[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2956095	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs2956097	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs2956112	0.82[CHB][hapmap]
rs2956116	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2956125	0.82[JPT][hapmap]
rs2985150	0.82[JPT][hapmap]
rs2985382	0.82[JPT][hapmap]
rs2986403	0.82[JPT][hapmap]
rs2986406	0.82[JPT][hapmap]
rs2986408	0.82[JPT][hapmap]
rs2986413	0.82[JPT][hapmap]
rs2986421	0.82[JPT][hapmap]
rs520658	0.82[JPT][hapmap]
rs724714	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs7932442	0.85[EUR][1000 genomes]
rs984690	0.82[CHD][hapmap];0.82[JPT][hapmap]

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	nsv832118	chr11:34743123-34903951	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv832119	chr11:34815528-35009370	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs1396880	PDHX	Cis_1M	lymphoblastoid	RTeQTL
rs1396880	APIP	cis	Nerve Tibial	GTEx
rs1396880	TRIM44	cis	cerebellum	SCAN
rs1396880	APIP	cis	multi-tissue	Pritchard
rs1396880	PDHX	cis	parietal	SCAN
rs1396880	MMRP19	cis	multi-tissue	Pritchard
rs1396880	APIP	cis	Artery Tibial	GTEx
rs1396880	APIP	cis	Thyroid	GTEx
rs1396880	APIP	cis	Skin Sun Exposed Lower leg	GTEx
rs1396880	APIP	cis	lung	GTEx
rs1396880	APIP	cis	Artery Aorta	GTEx
rs1396880	PDHX	cis	lymphoblastoid	seeQTL
rs1396880	APIP	cis	Esophagus Muscularis	GTEx
rs1396880	APIP	cis	brain	seeQTL
rs1396880	APIP	trans	brain	seeQTL
rs1396880	APIP	cis	lymphoblastoid	seeQTL
rs1396880	LOC728766///PRDM15	trans	lymphoblastoid	RTeQTL
rs1396880	APIP	cis	Heart Left Ventricle	GTEx
rs1396880	PDHX	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34859000-34909400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:34859400-34871800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:34869800-34871600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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