Variant report

Variant	rs4611216
Chromosome Location	chr11:120472667-120472668
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	chr11:120467473..120469063-chr11:120472319..120475182,2	K562	blood:
2	chr11:120471375..120475436-chr11:120476870..120481241,3	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10790388	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10892588	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11600274	0.91[ASN][1000 genomes]
rs11601552	0.87[ASN][1000 genomes]
rs11602011	0.84[ASN][1000 genomes]
rs11603831	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs11604139	0.81[ASN][1000 genomes]
rs11605735	0.87[ASN][1000 genomes]
rs12278532	0.86[ASN][1000 genomes]
rs1320721	0.91[EUR][1000 genomes]
rs34759019	0.87[ASN][1000 genomes]
rs34884722	0.87[ASN][1000 genomes]
rs4245039	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4331108	0.94[ASN][1000 genomes]
rs4367952	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4414229	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4936522	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4936523	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4936525	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4936526	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4936529	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6589819	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6589820	0.81[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6589821	0.91[ASN][1000 genomes]
rs7101412	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7111020	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7127199	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7934084	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7947677	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7949316	0.86[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7952478	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1036102	chr11:120442895-120498908	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv468881	chr11:120446830-120551100	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv556476	chr11:120446830-120551100	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4611216	BCL9L	cis	parietal	SCAN
rs4611216	C11orf63	cis	parietal	SCAN
rs4611216	AMICA1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120468600-120479400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr11:120468600-120479400	Weak transcription	Brain Substantia Nigra	brain
3	chr11:120469000-120473000	Enhancers	Fetal Lung	lung
4	chr11:120471000-120479400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:120471200-120479200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr11:120471400-120476400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:120471400-120479400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr11:120471800-120473000	Enhancers	Fetal Brain Male	brain
9	chr11:120471800-120476000	Weak transcription	GM12878-XiMat	blood
10	chr11:120472000-120472800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:120472000-120473200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr11:120472200-120473000	Enhancers	Brain Germinal Matrix	brain
13	chr11:120472200-120473400	Enhancers	NH-A	brain
14	chr11:120472400-120472800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:120472400-120473000	Enhancers	Fetal Brain Female	brain
16	chr11:120472400-120473200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr11:120472600-120472800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr11:120472600-120472800	Enhancers	Ovary	ovary
19	chr11:120472600-120472800	Enhancers	HSMM	muscle
20	chr11:120472600-120473000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:120472600-120479200	Weak transcription	Fetal Kidney	kidney

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