Variant report

Variant	rs17744711
Chromosome Location	chr11:85600724-85600725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10898417	0.80[CEU][hapmap]
rs11234457	1.00[CEU][hapmap]
rs11234458	1.00[CEU][hapmap]
rs11234462	1.00[CEU][hapmap]
rs11234463	1.00[CEU][hapmap]
rs11512932	1.00[CEU][hapmap]
rs11826218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11828105	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12271536	0.86[CEU][hapmap]
rs12280977	0.86[CEU][hapmap]
rs12361645	1.00[CEU][hapmap]
rs12361800	0.93[CEU][hapmap]
rs1445498	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1445500	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1445501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1445502	0.81[CEU][hapmap]
rs1445503	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1445504	1.00[ASW][hapmap];0.93[CEU][hapmap];0.93[GIH][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1445505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1445511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17744606	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17744675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17744699	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17817230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17817254	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17817308	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17817314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17817326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17817331	1.00[ASW][hapmap];1.00[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];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17817343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17817355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2044390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2084080	0.92[CEU][hapmap]
rs36093844	0.93[CEU][hapmap]
rs4015260	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4296062	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs55951560	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55978615	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56036199	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56202113	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56261432	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56396016	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59179556	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60135492	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7101889	0.81[CEU][hapmap]
rs7102361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7113656	0.81[CEU][hapmap]
rs7116742	1.00[JPT][hapmap]
rs7121363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7124956	0.81[CEU][hapmap]
rs7127478	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7127501	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7127873	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7931698	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7931771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7943104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7950738	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs895256	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv832222	chr11:85405712-85603981	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1035489	chr11:85502953-85778229	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1048818	chr11:85524635-85746473	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv541116	chr11:85524635-85746473	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv898051	chr11:85554057-85620823	Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	nsv898052	chr11:85579304-85620823	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv898053	chr11:85579304-85634425	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1053808	chr11:85588919-85757693	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17744711	PICALM	cis	cerebellum	SCAN
rs17744711	CCDC83	cis	parietal	SCAN
rs17744711	SYTL2	cis	cerebellum	SCAN
rs17744711	GRM5	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85595800-85601200	Weak transcription	HSMMtube	muscle
2	chr11:85596000-85600800	Weak transcription	HSMM	muscle
3	chr11:85596000-85601200	Weak transcription	NHLF	lung
4	chr11:85596400-85600800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:85596400-85600800	Weak transcription	NH-A	brain
6	chr11:85597800-85600800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:85597800-85600800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:85597800-85601000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr11:85597800-85601200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:85598000-85601000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:85598400-85600800	Weak transcription	NHDF-Ad	bronchial
12	chr11:85600000-85601400	Enhancers	HepG2	liver
13	chr11:85600200-85603400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr11:85600400-85601400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:85600400-85601800	Enhancers	A549	lung
16	chr11:85600400-85602200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr11:85600400-85602200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:85600600-85601400	Enhancers	H9 Cell Line	embryonic stem cell
19	chr11:85600600-85601600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr11:85600600-85601800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:85600600-85601800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr11:85600600-85601800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:85600600-85601800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr11:85600600-85601800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:85600600-85601800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:85600600-85601800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:85600600-85601800	Enhancers	Placenta	Placenta
28	chr11:85600600-85601800	Enhancers	Placenta Amnion	Placenta Amnion
29	chr11:85600600-85601800	Enhancers	Hela-S3	cervix
30	chr11:85600600-85601800	Enhancers	HMEC	breast
31	chr11:85600600-85601800	Enhancers	NHEK	skin
32	chr11:85600600-85601800	Enhancers	Osteobl	bone
33	chr11:85600600-85602000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:85600600-85602400	Enhancers	HUES6 Cell Line	embryonic stem cell

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