Variant report

Variant	rs2941057
Chromosome Location	chr11:34882220-34882221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:34880661..34882510-chr11:34884203..34886582,2	MCF-7	breast:
2	chr11:34870702..34874791-chr11:34878120..34882301,4	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1036070	0.84[ASN][1000 genomes]
rs1117051	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs1117445	0.84[ASN][1000 genomes]
rs1396880	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1396881	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1509662	0.81[ASN][1000 genomes]
rs1549789	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1549791	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1553757	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1553758	0.81[ASN][1000 genomes]
rs1553759	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1553760	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1553761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1553762	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1828298	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1858166	0.81[ASN][1000 genomes]
rs1960524	0.93[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1991648	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2031686	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2033355	0.84[ASN][1000 genomes]
rs2033357	0.84[ASN][1000 genomes]
rs2033358	0.84[ASN][1000 genomes]
rs2033360	0.84[ASN][1000 genomes]
rs2116085	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2116090	0.84[ASN][1000 genomes]
rs2147341	0.81[ASN][1000 genomes]
rs2163374	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2163375	0.89[ASN][1000 genomes]
rs2421743	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915177	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915178	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2915179	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2915180	0.81[ASN][1000 genomes]
rs2915198	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs2915208	0.84[ASN][1000 genomes]
rs2915214	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2915217	0.93[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2915218	0.84[ASN][1000 genomes]
rs2915225	0.93[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2915226	0.84[ASN][1000 genomes]
rs2915228	0.84[ASN][1000 genomes]
rs2915230	0.84[ASN][1000 genomes]
rs2915231	0.84[ASN][1000 genomes]
rs2915232	0.84[ASN][1000 genomes]
rs2915233	0.84[ASN][1000 genomes]
rs2915235	0.84[ASN][1000 genomes]
rs2915237	0.89[ASN][1000 genomes]
rs2915238	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2941040	0.94[ASN][1000 genomes]
rs2941041	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2941042	0.81[ASN][1000 genomes]
rs2941043	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2941044	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2941050	0.84[ASN][1000 genomes]
rs2941052	0.84[ASN][1000 genomes]
rs2941054	0.95[ASN][1000 genomes]
rs2941055	0.83[ASN][1000 genomes]
rs2941056	0.98[ASN][1000 genomes]
rs2941058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2941059	0.88[ASN][1000 genomes]
rs2941060	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2941061	0.84[ASN][1000 genomes]
rs2956074	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2956076	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2956077	0.81[JPT][hapmap]
rs2956078	0.97[ASN][1000 genomes]
rs2956079	0.89[ASN][1000 genomes]
rs2956080	0.84[ASN][1000 genomes]
rs2956084	0.84[ASN][1000 genomes]
rs2956086	1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs2956095	1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2956097	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2956109	0.82[ASN][1000 genomes]
rs2956112	0.92[CHB][hapmap]
rs2956116	0.93[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2956118	0.82[ASN][1000 genomes]
rs2956120	0.84[ASN][1000 genomes]
rs2956125	0.93[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2985150	0.81[JPT][hapmap]
rs2985382	0.93[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2986403	0.81[JPT][hapmap]
rs2986406	0.81[JPT][hapmap]
rs2986408	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2986413	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2986415	0.82[ASN][1000 genomes]
rs2986417	0.82[ASN][1000 genomes]
rs2986421	0.93[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs520658	0.81[JPT][hapmap]
rs724714	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7932442	0.83[EUR][1000 genomes]
rs891550	0.84[ASN][1000 genomes]
rs919554	0.84[ASN][1000 genomes]
rs925289	0.84[ASN][1000 genomes]
rs984690	0.93[CHB][hapmap];0.81[JPT][hapmap];0.82[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	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2941057	LOC728766///PRDM15	trans	lymphoblastoid	RTeQTL
rs2941057	APIP	cis	Esophagus Muscularis	GTEx
rs2941057	APIP	cis	Heart Left Ventricle	GTEx
rs2941057	APIP	cis	lung	GTEx
rs2941057	APIP	cis	Thyroid	GTEx
rs2941057	APIP	cis	multi-tissue	Pritchard
rs2941057	APIP	cis	Artery Aorta	GTEx
rs2941057	APIP	cis	Lymphoblastoid	GTEx
rs2941057	APIP	cis	Nerve Tibial	GTEx
rs2941057	PDHX	Cis_1M	lymphoblastoid	RTeQTL
rs2941057	APIP	cis	Artery Tibial	GTEx
rs2941057	APIP	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:20 , 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	chr11:34872200-34886600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:34876600-34896000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:34877400-34886400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr11:34877600-34906400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:34878200-34891400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:34880200-34898000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:34880400-34882400	Enhancers	Esophagus	oesophagus
9	chr11:34880600-34884200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:34880800-34882400	Enhancers	Fetal Heart	heart
11	chr11:34880800-34882600	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr11:34881000-34882400	Enhancers	Adipose Nuclei	Adipose
13	chr11:34881000-34882600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:34881000-34882600	Enhancers	Fetal Lung	lung
15	chr11:34881000-34882600	Enhancers	Fetal Muscle Leg	muscle
16	chr11:34881600-34882400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:34881600-34882400	Enhancers	Psoas Muscle	Psoas
18	chr11:34881600-34882400	Enhancers	HSMMtube	muscle
19	chr11:34882000-34882400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr11:34882000-34919800	Weak transcription	Left Ventricle	heart

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