Variant report

Variant	rs17245580
Chromosome Location	chr11:120480883-120480884
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	chr11:120471375..120475436-chr11:120476870..120481241,3	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11217924	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12274778	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1316812	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1317814	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1317815	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4375451	0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs4935743	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4935744	0.95[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs4936528	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4936533	0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs56763747	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58047799	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59127761	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60787798	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61900926	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7131215	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73002644	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73002650	0.87[AMR][1000 genomes];0.98[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17245580	C1QTNF5	cis	parietal	SCAN
rs17245580	ASAM	cis	parietal	SCAN
rs17245580	FXYD6	cis	cerebellum	SCAN
rs17245580	BCL9L	cis	parietal	SCAN
rs17245580	PDZD3	cis	parietal	SCAN
rs17245580	BUD13	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120475000-120481400	Enhancers	Fetal Lung	lung
2	chr11:120476400-120482600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:120478200-120481600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr11:120478200-120482000	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr11:120478400-120481400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:120478400-120482400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr11:120478600-120481600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr11:120478800-120481200	Weak transcription	GM12878-XiMat	blood
9	chr11:120478800-120484400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:120479000-120481200	Enhancers	Fetal Brain Female	brain
11	chr11:120479000-120481600	Enhancers	Brain Hippocampus Middle	brain
12	chr11:120479200-120483600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr11:120479400-120481600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr11:120479400-120481600	Enhancers	Fetal Stomach	stomach
15	chr11:120479400-120482200	Enhancers	Fetal Brain Male	brain
16	chr11:120479800-120482200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr11:120479800-120484000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:120479800-120484800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr11:120480000-120481600	Weak transcription	Adipose Nuclei	Adipose
20	chr11:120480000-120482200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:120480000-120483400	Weak transcription	Fetal Intestine Large	intestine
22	chr11:120480000-120483400	Weak transcription	Fetal Intestine Small	intestine
23	chr11:120480200-120481200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr11:120480200-120483400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:120480200-120483400	Weak transcription	Ovary	ovary
26	chr11:120480200-120484600	Weak transcription	Right Atrium	heart
27	chr11:120480200-120487600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:120480200-120489000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr11:120480400-120482600	Enhancers	H9 Cell Line	embryonic stem cell
30	chr11:120480600-120481400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:120480600-120481600	Enhancers	Fetal Kidney	kidney
32	chr11:120480600-120482400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr11:120480800-120481400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:120480800-120481400	Enhancers	Pancreas	Pancrea
35	chr11:120480800-120482800	Enhancers	Spleen	Spleen

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