Variant report

Variant	rs1541309
Chromosome Location	chr11:86301957-86301958
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	chr11:86299123..86300759-chr11:86301620..86304083,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10501627	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10501628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10898508	0.89[ASN][1000 genomes]
rs11234705	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11234707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234708	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11606017	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs12365092	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12790474	1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12804997	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1540083	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs1541308	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938922	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4382935	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944571	1.00[JPT][hapmap]
rs4944576	1.00[JPT][hapmap]
rs4944614	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7930619	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv898056	chr11:86156848-86304402	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv555678	chr11:86285994-86305977	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1541309	PICALM	cis	parietal	SCAN
rs1541309	ME3	cis	multi-tissue	Pritchard
rs1541309	CTSC	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86289800-86303200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr11:86289800-86303400	Weak transcription	Stomach Mucosa	stomach
3	chr11:86292000-86303800	Weak transcription	Ovary	ovary
4	chr11:86292200-86303200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr11:86292800-86303800	Weak transcription	Gastric	stomach
6	chr11:86293400-86303800	Weak transcription	Aorta	Aorta
7	chr11:86294200-86303800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr11:86294400-86303400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr11:86295600-86303400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:86297400-86308000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr11:86298000-86302200	Weak transcription	Fetal Intestine Large	intestine
12	chr11:86298000-86307000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:86298200-86304600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr11:86298200-86307400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:86298400-86303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:86298600-86302400	Weak transcription	HMEC	breast
17	chr11:86298600-86303400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr11:86298800-86304400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr11:86299200-86304600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr11:86299400-86302200	Enhancers	Psoas Muscle	Psoas
21	chr11:86299400-86304800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:86299600-86302000	Enhancers	Left Ventricle	heart
23	chr11:86299600-86302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr11:86300000-86303400	Weak transcription	Brain Anterior Caudate	brain
25	chr11:86300000-86303800	Weak transcription	Spleen	Spleen
26	chr11:86300000-86304000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr11:86300200-86302200	Weak transcription	HUVEC	blood vessel
28	chr11:86300200-86302800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:86300200-86302800	Weak transcription	Fetal Lung	lung
30	chr11:86300200-86303000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr11:86300200-86303000	Weak transcription	NHDF-Ad	bronchial
32	chr11:86300200-86303200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr11:86300200-86303200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr11:86300200-86303800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:86300200-86303800	Weak transcription	Small Intestine	intestine
36	chr11:86300200-86305400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr11:86300200-86308200	Weak transcription	Fetal Brain Male	brain
38	chr11:86300200-86318800	Weak transcription	Esophagus	oesophagus
39	chr11:86300400-86302400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr11:86300400-86302800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr11:86300400-86303200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr11:86300400-86303200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr11:86300400-86303200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr11:86300400-86303600	Weak transcription	Brain Germinal Matrix	brain
45	chr11:86300400-86303800	Weak transcription	Adipose Nuclei	Adipose
46	chr11:86300600-86302200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr11:86300600-86302400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr11:86300600-86303400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr11:86300600-86303400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr11:86300600-86304200	Enhancers	Placenta Amnion	Placenta Amnion

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