Variant report

Variant	rs11077542
Chromosome Location	chr17:66399104-66399105
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:66390902..66393110-chr17:66399070..66401474,2	MCF-7	breast:
2	chr17:66283412..66291453-chr17:66391949..66401713,36	MCF-7	breast:
3	chr17:66398317..66401303-chr17:66414523..66417080,2	MCF-7	breast:
4	chr17:66395376..66396896-chr17:66398197..66400671,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141337	Chromatin interaction
ENSG00000108932	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1002446	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs11870010	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12453020	0.86[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12943181	0.87[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12945490	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12946747	0.87[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12947036	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12948224	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59439636	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11077542	NOL11	cis	cerebellum	SCAN
rs11077542	SMARCD2	cis	parietal	SCAN
rs11077542	CCDC47	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66395200-66401800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr17:66395200-66416000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr17:66395400-66399600	Weak transcription	Brain Anterior Caudate	brain
4	chr17:66395400-66415800	Weak transcription	Right Ventricle	heart
5	chr17:66395600-66409800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr17:66395600-66410000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr17:66396000-66399200	Weak transcription	Adipose Nuclei	Adipose
8	chr17:66396000-66401000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:66396200-66400200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr17:66396400-66399400	Weak transcription	Psoas Muscle	Psoas
11	chr17:66396600-66399200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr17:66396800-66399400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr17:66396800-66409800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr17:66397000-66401000	Weak transcription	Dnd41	blood
15	chr17:66397000-66401600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr17:66397000-66402200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr17:66397200-66401000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr17:66397200-66401400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr17:66397800-66400000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr17:66397800-66410000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:66398000-66410000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr17:66399000-66399600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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