Variant report

Variant	rs17744938
Chromosome Location	chr11:85676566-85676567
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85674041..85677352-chr11:85678170..85681418,4	K562	blood:
2	chr11:85675116..85677368-chr11:85679918..85681449,2	K562	blood:
3	chr11:85658393..85662131-chr11:85674389..85678033,3	K562	blood:
4	chr11:85668411..85669931-chr11:85676014..85677622,2	K562	blood:
5	chr11:85667493..85669931-chr11:85675862..85677514,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10128700	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10501603	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10501605	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10501607	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10501610	1.00[LWK][hapmap]
rs10898431	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs11234489	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11234492	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11234496	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11234502	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11234512	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11234513	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11234517	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11234544	0.88[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap]
rs12270433	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12278260	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12279956	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12281494	0.82[EUR][1000 genomes]
rs12281958	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12282655	0.88[EUR][1000 genomes]
rs12284629	0.94[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap]
rs12287170	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12294130	0.82[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap]
rs1596739	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17159904	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs17745105	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17745153	0.94[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17745236	0.93[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17745248	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17745273	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17817582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17817588	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17817690	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17817859	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17817883	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17817919	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17817956	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2001241	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2084077	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41381550	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4943934	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4943936	0.91[AMR][1000 genomes]
rs4943937	0.93[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs4944550	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4944551	0.93[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4944552	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4944553	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4944554	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4944555	0.92[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4944556	0.94[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs55697624	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55791429	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55815523	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56026701	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56187740	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57125313	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58937798	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72949419	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72949429	0.85[AMR][1000 genomes]
rs72949443	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72950443	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72950453	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72950456	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72951266	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72951268	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72959177	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72959197	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72959906	0.82[EUR][1000 genomes]
rs72961110	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72961111	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72963077	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72963086	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72963092	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72965157	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72965166	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7927222	0.88[CEU][hapmap];0.86[GIH][hapmap]
rs7943152	0.94[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
4	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
5	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
6	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
7	nsv1053599	chr11:85641619-85684353	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv1040567	chr11:85641619-85684935	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17744938	PICALM	cis	cerebellum	SCAN
rs17744938	CCDC83	cis	parietal	SCAN
rs17744938	FAM181B	cis	parietal	SCAN
rs17744938	GRM5	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85656000-85679800	Weak transcription	Fetal Brain Male	brain
2	chr11:85659400-85745800	Weak transcription	Stomach Mucosa	stomach
3	chr11:85663400-85692000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:85663800-85740200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:85664400-85678600	Strong transcription	Adipose Nuclei	Adipose
6	chr11:85664400-85687200	Strong transcription	Primary T cells from cord blood	blood
7	chr11:85664400-85693600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr11:85664400-85699800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr11:85664400-85726800	Strong transcription	Liver	Liver
10	chr11:85664400-85729000	Strong transcription	Placenta	Placenta
11	chr11:85664600-85693200	Strong transcription	Fetal Thymus	thymus
12	chr11:85664600-85730800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:85664800-85678600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:85664800-85689400	Strong transcription	Primary B cells from cord blood	blood
15	chr11:85664800-85733000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:85665000-85679200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:85665200-85742600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr11:85665200-85743000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:85665400-85678800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr11:85665400-85699800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr11:85665600-85679600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:85665600-85687800	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr11:85665800-85679600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:85665800-85699600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr11:85665800-85701200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr11:85665800-85711400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:85666000-85677200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:85666000-85679200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr11:85666000-85735800	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr11:85666400-85679000	Strong transcription	Hela-S3	cervix
31	chr11:85666400-85679200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr11:85666400-85680400	Strong transcription	Dnd41	blood
33	chr11:85666400-85693600	Strong transcription	Primary hematopoietic stem cells	blood
34	chr11:85666600-85680200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:85666800-85679400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:85667800-85678800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:85667800-85679200	Strong transcription	NHLF	lung
38	chr11:85667800-85701800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:85667800-85712000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr11:85668000-85677200	Weak transcription	Ovary	ovary
41	chr11:85668000-85681600	Weak transcription	Fetal Brain Female	brain
42	chr11:85668000-85691400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr11:85669400-85686200	Strong transcription	Fetal Intestine Large	intestine
44	chr11:85670000-85715800	Weak transcription	Colonic Mucosa	Colon
45	chr11:85670400-85678800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr11:85670600-85677200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:85670600-85679200	Strong transcription	Thymus	Thymus
48	chr11:85671200-85678600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr11:85671600-85677800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:85671800-85710600	Weak transcription	Psoas Muscle	Psoas

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