Variant report

Variant	rs676733
Chromosome Location	chr11:85734010-85734011
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr11:85733966-85734064	K562	blood:	n/a	n/a
2	POLR2A	chr11:85729904-85736468	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85725973..85728229-chr11:85733987..85735840,2	K562	blood:
2	chr11:85734003..85736029-chr11:85992603..85995155,2	K562	blood:

Variant related genes	Relation type
PICALM	TF binding region
ENSG00000254783	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10751134	0.90[JPT][hapmap]
rs10792830	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs10792831	0.81[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs10792832	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10898438	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs10898439	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs1214669	0.84[ASN][1000 genomes]
rs12808312	0.85[ASN][1000 genomes]
rs1898895	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1949221	0.99[ASN][1000 genomes]
rs1973630	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2508381	0.99[ASN][1000 genomes]
rs2508688	0.84[AFR][1000 genomes]
rs2508690	0.90[ASN][1000 genomes]
rs2508691	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2508692	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2508693	0.94[ASN][1000 genomes]
rs2508696	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2508697	0.84[ASN][1000 genomes]
rs3016240	0.93[ASN][1000 genomes]
rs3016786	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3851178	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs3851179	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs475639	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs478711	0.88[ASN][1000 genomes]
rs480781	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs484154	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs489486	0.82[AFR][1000 genomes]
rs493254	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4944560	0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs497816	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs501505	0.87[ASN][1000 genomes]
rs519778	0.92[ASN][1000 genomes]
rs526904	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs527162	0.87[ASW][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap]
rs529904	0.95[ASN][1000 genomes]
rs532470	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs535590	0.85[EUR][1000 genomes]
rs536841	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs541458	0.92[CEU][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs541674	0.99[ASN][1000 genomes]
rs542126	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs545592	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs553141	0.98[ASN][1000 genomes]
rs561646	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs561655	0.84[GIH][hapmap]
rs563773	0.92[ASN][1000 genomes]
rs565031	0.91[ASN][1000 genomes]
rs565719	0.87[EUR][1000 genomes]
rs585820	0.82[AFR][1000 genomes]
rs587038	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588076	1.00[ASW][hapmap];0.89[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs592297	0.87[ASW][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap]
rs601185	0.82[YRI][hapmap]
rs602222	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs603615	0.82[AFR][1000 genomes]
rs606505	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs609903	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613222	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs618629	0.84[AFR][1000 genomes]
rs629343	0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs631639	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs636355	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636772	0.95[ASN][1000 genomes]
rs639012	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs642949	0.96[ASN][1000 genomes]
rs645299	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs647422	0.92[ASN][1000 genomes]
rs655641	0.84[AFR][1000 genomes]
rs659023	0.86[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap]
rs659863	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs666682	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs669556	0.81[MKK][hapmap]
rs669813	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs671686	0.89[ASN][1000 genomes]
rs673751	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs677869	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs677909	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs682928	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs683494	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs694011	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7114331	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs7114401	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7129687	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs7941541	0.87[ASW][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap]
rs7951988	0.85[CHB][hapmap]
rs867611	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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
rs676733	PICALM	cis	cerebellum	SCAN

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	chr11:85665200-85742600	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:85665200-85743000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr11:85666000-85735800	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr11:85675000-85742600	Strong transcription	Primary B cells from peripheral blood	blood
7	chr11:85697800-85742600	Strong transcription	HUVEC	blood vessel
8	chr11:85700600-85742400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:85701000-85745000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:85703200-85742800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:85712600-85736200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:85712800-85735800	Weak transcription	Esophagus	oesophagus
13	chr11:85712800-85740800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:85712800-85741600	Weak transcription	Aorta	Aorta
15	chr11:85712800-85743400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr11:85713000-85734600	Weak transcription	Fetal Brain Male	brain
17	chr11:85714000-85735600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:85714600-85734400	Weak transcription	Small Intestine	intestine
19	chr11:85716600-85741400	Weak transcription	Fetal Heart	heart
20	chr11:85716800-85736200	Weak transcription	Lung	lung
21	chr11:85716800-85746200	Weak transcription	Pancreas	Pancrea
22	chr11:85717600-85739800	Weak transcription	Psoas Muscle	Psoas
23	chr11:85718000-85738400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr11:85718200-85736200	Weak transcription	Gastric	stomach
25	chr11:85719800-85736800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr11:85719800-85743400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:85720200-85735600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr11:85720400-85742600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:85720800-85736000	Weak transcription	Spleen	Spleen
30	chr11:85720800-85742600	Strong transcription	HSMM	muscle
31	chr11:85721200-85734600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:85721800-85734400	Weak transcription	Left Ventricle	heart
33	chr11:85721800-85734800	Weak transcription	Fetal Stomach	stomach
34	chr11:85721800-85736200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:85721800-85738600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:85721800-85745800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr11:85725200-85736800	Weak transcription	Colonic Mucosa	Colon
38	chr11:85725600-85734200	Weak transcription	A549	lung
39	chr11:85725600-85742800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:85726200-85736800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr11:85727200-85736200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr11:85727200-85741800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:85727200-85742000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:85727600-85735600	Weak transcription	Brain Angular Gyrus	brain
45	chr11:85727800-85735800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr11:85727800-85741800	Strong transcription	Liver	Liver
47	chr11:85727800-85745800	Weak transcription	Right Ventricle	heart
48	chr11:85728000-85735600	Weak transcription	HSMMtube	muscle
49	chr11:85728000-85736800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr11:85728200-85734400	Weak transcription	Thymus	Thymus

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