Variant report

Variant	rs2941040
Chromosome Location	chr11:34874780-34874781
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:34870702..34874791-chr11:34878120..34882301,4	K562	blood:

Extended variants
information (count: 105 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10836322	0.83[EUR][1000 genomes]
rs11032916	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1117051	0.86[CHB][hapmap]
rs1396880	0.92[ASN][1000 genomes]
rs1396881	0.92[ASN][1000 genomes]
rs1549789	0.92[ASN][1000 genomes]
rs1553757	0.92[ASN][1000 genomes]
rs1553758	0.82[ASN][1000 genomes]
rs1553759	0.93[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs1553760	0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1553761	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1553762	0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1571135	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1828298	0.92[ASN][1000 genomes]
rs1858166	0.82[ASN][1000 genomes]
rs1960524	0.93[CHB][hapmap]
rs1977420	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1991648	0.86[CHB][hapmap]
rs2016821	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2031686	0.86[CHB][hapmap]
rs2031687	0.83[EUR][1000 genomes]
rs2033355	0.84[ASN][1000 genomes]
rs2116084	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2163374	0.92[ASN][1000 genomes]
rs2163375	0.83[ASN][1000 genomes]
rs2303958	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2303959	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2421743	0.94[ASN][1000 genomes]
rs2915177	0.94[ASN][1000 genomes]
rs2915178	0.95[ASN][1000 genomes]
rs2915179	0.92[ASN][1000 genomes]
rs2915180	0.82[ASN][1000 genomes]
rs2915190	0.81[EUR][1000 genomes]
rs2915193	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2915198	0.84[CHB][hapmap]
rs2915204	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2915205	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2915206	0.81[EUR][1000 genomes]
rs2915214	0.86[CHB][hapmap]
rs2915215	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2915216	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2915217	0.93[CHB][hapmap]
rs2915225	0.93[CHB][hapmap]
rs2915234	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2915236	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2915237	0.83[ASN][1000 genomes]
rs2915238	0.94[ASN][1000 genomes]
rs2941041	0.97[ASN][1000 genomes]
rs2941042	0.82[ASN][1000 genomes]
rs2941043	0.92[ASN][1000 genomes]
rs2941044	0.97[ASN][1000 genomes]
rs2941048	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2941049	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2941054	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2941056	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2941057	0.94[ASN][1000 genomes]
rs2941058	0.94[ASN][1000 genomes]
rs2941059	0.84[ASN][1000 genomes]
rs2941060	0.90[ASN][1000 genomes]
rs2956074	0.95[ASN][1000 genomes]
rs2956076	0.92[ASN][1000 genomes]
rs2956078	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2956079	0.83[ASN][1000 genomes]
rs2956082	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2956083	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2956086	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2956087	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs2956089	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2956094	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2956095	1.00[CHB][hapmap]
rs2956097	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2956107	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2956111	0.85[EUR][1000 genomes]
rs2956112	0.92[CHB][hapmap]
rs2956113	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2956114	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2956116	0.93[CHB][hapmap]
rs2956117	0.83[EUR][1000 genomes]
rs2956125	0.93[CHB][hapmap]
rs2985382	0.93[CHB][hapmap]
rs2985384	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2985388	0.88[EUR][1000 genomes]
rs2985390	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2985400	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2985404	0.83[EUR][1000 genomes]
rs2985405	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2986404	0.81[EUR][1000 genomes]
rs2986408	0.85[CHB][hapmap]
rs2986409	0.83[EUR][1000 genomes]
rs2986410	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2986413	0.86[CHB][hapmap]
rs2986414	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2986416	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2986419	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2986420	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2986421	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs2986425	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2986426	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2986427	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2986428	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs724714	0.85[CHB][hapmap]
rs891546	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs984690	0.93[CHB][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2941040	APIP	cis	Lymphoblastoid	GTEx
rs2941040	APIP	cis	multi-tissue	Pritchard
rs2941040	PDHX	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 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	chr11:34871600-34875600	Weak transcription	Small Intestine	intestine
3	chr11:34872000-34875600	Weak transcription	Fetal Intestine Large	intestine
4	chr11:34872200-34886600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:34872400-34875400	Weak transcription	Stomach Mucosa	stomach
6	chr11:34872600-34875600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr11:34872600-34875800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr11:34872800-34876600	Weak transcription	Hela-S3	cervix
9	chr11:34873200-34875200	Weak transcription	Rectal Mucosa Donor 31	rectum

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