Variant report

Variant	rs4141260
Chromosome Location	chr11:17708242-17708243
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:17701946..17705746-chr11:17707792..17711044,3	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10741731	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10766418	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10766419	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10766421	0.91[EUR][1000 genomes]
rs10832837	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10832841	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10832844	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11024364	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024367	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024368	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024375	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11605342	0.82[AFR][1000 genomes]
rs11605964	0.91[EUR][1000 genomes]
rs12785437	0.88[ASN][1000 genomes]
rs16934571	0.85[ASN][1000 genomes]
rs2526551	0.82[EUR][1000 genomes]
rs28683112	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2878806	0.93[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.92[YRI][hapmap];0.88[ASN][1000 genomes]
rs2878807	0.88[ASN][1000 genomes]
rs3858499	0.88[ASN][1000 genomes]
rs3858501	0.88[ASN][1000 genomes]
rs3858502	0.88[ASN][1000 genomes]
rs3901370	1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs3935159	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4081578	0.81[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs4141261	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4141262	0.88[EUR][1000 genomes]
rs4756905	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4756907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757565	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4757567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757568	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4757569	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7395942	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7483014	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9633896	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040065	chr11:17556031-17753467	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1044126	chr11:17557715-17730646	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv540953	chr11:17557715-17730646	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4141260	SAA2	cis	parietal	SCAN
rs4141260	DKFZp686O24166	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17704000-17711600	Enhancers	Skeletal Muscle Male	skeletal muscle
2	chr11:17704200-17711600	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr11:17705600-17709400	Enhancers	HSMM	muscle
4	chr11:17706000-17708800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr11:17707400-17708400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:17707600-17708400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:17707600-17709800	Enhancers	HSMMtube	muscle
8	chr11:17707600-17712200	Enhancers	Fetal Muscle Leg	muscle
9	chr11:17708000-17708400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:17708000-17709000	Weak transcription	Psoas Muscle	Psoas
11	chr11:17708000-17711400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:17708200-17709200	Weak transcription	Fetal Muscle Trunk	muscle

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