Variant report

Variant	rs1949221
Chromosome Location	chr11:85732690-85732691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1214669	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12808312	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1973630	0.84[ASN][1000 genomes]
rs2508381	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508690	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2508691	0.88[ASN][1000 genomes]
rs2508692	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2508693	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2508696	0.96[ASN][1000 genomes]
rs2508697	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3016240	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3016786	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs475639	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs478711	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs484154	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs493254	0.88[ASN][1000 genomes]
rs501505	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs519778	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs529904	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs532470	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs541674	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs545592	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs553141	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs561646	0.97[ASN][1000 genomes]
rs563773	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs565031	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs572979	0.85[EUR][1000 genomes]
rs579406	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs587038	0.95[ASN][1000 genomes]
rs602222	0.96[ASN][1000 genomes]
rs604767	0.89[EUR][1000 genomes]
rs606505	0.95[ASN][1000 genomes]
rs609903	0.99[ASN][1000 genomes]
rs613222	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs636355	0.99[ASN][1000 genomes]
rs636772	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs639012	0.89[ASN][1000 genomes]
rs642949	0.97[ASN][1000 genomes]
rs645299	0.96[ASN][1000 genomes]
rs647422	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs659863	0.93[ASN][1000 genomes]
rs666682	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs669813	0.88[ASN][1000 genomes]
rs671686	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs673751	0.91[ASN][1000 genomes]
rs676733	0.99[ASN][1000 genomes]
rs677869	0.93[ASN][1000 genomes]
rs677909	0.93[ASN][1000 genomes]
rs682928	0.94[ASN][1000 genomes]
rs683494	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs694011	0.92[ASN][1000 genomes]
rs867611	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv468769	chr11:85683554-85757589	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv555641	chr11:85683554-85757589	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv898054	chr11:85683554-85772636	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv468770	chr11:85688209-85751883	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv555642	chr11:85688209-85751883	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv468771	chr11:85688209-85757589	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv468773	chr11:85688209-85757589	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv555643	chr11:85688209-85757589	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv468774	chr11:85688209-85775059	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv555644	chr11:85688209-85775059	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1949221	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85659400-85745800	Weak transcription	Stomach Mucosa	stomach
2	chr11:85663800-85740200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:85664800-85733000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:85665200-85742600	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr11:85665200-85743000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:85666000-85735800	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr11:85675000-85742600	Strong transcription	Primary B cells from peripheral blood	blood
8	chr11:85697400-85733400	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr11:85697800-85742600	Strong transcription	HUVEC	blood vessel
10	chr11:85700600-85742400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:85701000-85745000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:85703200-85742800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:85712600-85736200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:85712800-85735800	Weak transcription	Esophagus	oesophagus
15	chr11:85712800-85740800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:85712800-85741600	Weak transcription	Aorta	Aorta
17	chr11:85712800-85743400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:85713000-85734600	Weak transcription	Fetal Brain Male	brain
19	chr11:85714000-85735600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:85714600-85734400	Weak transcription	Small Intestine	intestine
21	chr11:85715800-85733200	Strong transcription	Fetal Intestine Large	intestine
22	chr11:85716600-85741400	Weak transcription	Fetal Heart	heart
23	chr11:85716800-85736200	Weak transcription	Lung	lung
24	chr11:85716800-85746200	Weak transcription	Pancreas	Pancrea
25	chr11:85717600-85739800	Weak transcription	Psoas Muscle	Psoas
26	chr11:85718000-85738400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr11:85718200-85736200	Weak transcription	Gastric	stomach
28	chr11:85719800-85736800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr11:85719800-85743400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr11:85720200-85735600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:85720400-85733600	Strong transcription	Hela-S3	cervix
32	chr11:85720400-85742600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:85720800-85736000	Weak transcription	Spleen	Spleen
34	chr11:85720800-85742600	Strong transcription	HSMM	muscle
35	chr11:85721200-85734600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:85721800-85734400	Weak transcription	Left Ventricle	heart
37	chr11:85721800-85734800	Weak transcription	Fetal Stomach	stomach
38	chr11:85721800-85736200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:85721800-85738600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr11:85721800-85745800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr11:85722600-85732800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr11:85725200-85736800	Weak transcription	Colonic Mucosa	Colon
43	chr11:85725600-85734200	Weak transcription	A549	lung
44	chr11:85725600-85742800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:85726200-85736800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr11:85726600-85733400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr11:85726800-85733000	Strong transcription	Primary B cells from cord blood	blood
48	chr11:85727000-85733000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr11:85727200-85736200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr11:85727200-85741800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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