Variant report

Variant	rs41381550
Chromosome Location	chr11:85667088-85667089
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85661662..85663622-chr11:85665077..85667243,2	K562	blood:
2	chr11:85664911..85667444-chr11:85667862..85673209,4	K562	blood:
3	chr11:85664911..85667241-chr11:85670910..85673209,2	K562	blood:
4	chr11:85666636..85668318-chr11:85679580..85681580,2	K562	blood:

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10128700	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10501603	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10501605	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10501607	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10501610	1.00[LWK][hapmap]
rs10898431	0.88[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234441	1.00[ASN][1000 genomes]
rs11234489	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234492	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234496	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234502	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234512	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234513	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234517	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234522	1.00[ASN][1000 genomes]
rs11234544	0.82[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap]
rs11825378	1.00[ASN][1000 genomes]
rs11825912	1.00[ASN][1000 genomes]
rs11828161	1.00[ASN][1000 genomes]
rs12270433	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12278260	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12279581	1.00[ASN][1000 genomes]
rs12279956	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12281958	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12282655	0.85[EUR][1000 genomes]
rs12284629	0.88[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap]
rs12287170	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12294130	1.00[GIH][hapmap];0.97[TSI][hapmap]
rs1596739	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17148600	1.00[ASN][1000 genomes]
rs17159904	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs17744938	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17745105	0.94[CEU][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17745153	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17745236	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17745248	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17745273	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17817582	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17817588	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17817690	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17817859	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17817883	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17817919	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];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17817956	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2001241	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2084077	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4943934	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4943936	0.87[AMR][1000 genomes]
rs4943937	0.85[CEU][hapmap]
rs4944550	0.94[CEU][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4944551	0.87[CEU][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4944552	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944553	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4944554	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4944555	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4944556	0.88[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap]
rs55697624	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55791429	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55815523	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56026701	0.88[EUR][1000 genomes]
rs56187740	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56944537	1.00[ASN][1000 genomes]
rs57125313	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58515881	1.00[ASN][1000 genomes]
rs58937798	0.88[EUR][1000 genomes]
rs59019168	1.00[ASN][1000 genomes]
rs59104711	1.00[ASN][1000 genomes]
rs60185300	0.82[AMR][1000 genomes]
rs60253048	1.00[ASN][1000 genomes]
rs60264644	1.00[ASN][1000 genomes]
rs60737637	1.00[ASN][1000 genomes]
rs61535933	1.00[ASN][1000 genomes]
rs72947601	0.82[AMR][1000 genomes]
rs72949419	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72949429	0.89[AMR][1000 genomes]
rs72949443	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72950443	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72950453	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72950456	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72951266	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72951268	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959177	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959197	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72961110	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72961111	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72963077	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72963086	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72963092	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72965157	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72965166	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7927222	0.82[CEU][hapmap];0.86[GIH][hapmap];0.82[AMR][1000 genomes]
rs7943152	0.87[CEU][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs41381550	FAM181B	cis	parietal	SCAN
rs41381550	PICALM	cis	cerebellum	SCAN
rs41381550	SYTL2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85646600-85667400	Weak transcription	Gastric	stomach
2	chr11:85652800-85668800	Weak transcription	Small Intestine	intestine
3	chr11:85656000-85679800	Weak transcription	Fetal Brain Male	brain
4	chr11:85658400-85667400	Weak transcription	Pancreas	Pancrea
5	chr11:85658600-85667400	Weak transcription	Esophagus	oesophagus
6	chr11:85658600-85673000	Weak transcription	Right Ventricle	heart
7	chr11:85659400-85745800	Weak transcription	Stomach Mucosa	stomach
8	chr11:85660200-85670800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:85660400-85667400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:85663400-85692000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:85663800-85740200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr11:85664200-85668200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:85664200-85673000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:85664400-85667200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:85664400-85667600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:85664400-85667600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:85664400-85667800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:85664400-85667800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:85664400-85668000	Enhancers	Ovary	ovary
20	chr11:85664400-85668200	Strong transcription	Fetal Intestine Large	intestine
21	chr11:85664400-85673000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:85664400-85678600	Strong transcription	Adipose Nuclei	Adipose
23	chr11:85664400-85687200	Strong transcription	Primary T cells from cord blood	blood
24	chr11:85664400-85693600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:85664400-85699800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr11:85664400-85726800	Strong transcription	Liver	Liver
27	chr11:85664400-85729000	Strong transcription	Placenta	Placenta
28	chr11:85664600-85667800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr11:85664600-85668000	Strong transcription	Fetal Stomach	stomach
30	chr11:85664600-85668000	Strong transcription	Thymus	Thymus
31	chr11:85664600-85673000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:85664600-85693200	Strong transcription	Fetal Thymus	thymus
33	chr11:85664600-85730800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:85664800-85674200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:85664800-85678600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr11:85664800-85689400	Strong transcription	Primary B cells from cord blood	blood
37	chr11:85664800-85733000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr11:85665000-85667600	Genic enhancers	Osteobl	bone
39	chr11:85665000-85668000	Genic enhancers	Fetal Muscle Leg	muscle
40	chr11:85665000-85671000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:85665000-85673600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:85665000-85679200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr11:85665200-85667200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr11:85665200-85668000	Strong transcription	Fetal Brain Female	brain
45	chr11:85665200-85668400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr11:85665200-85668800	Weak transcription	Fetal Kidney	kidney
47	chr11:85665200-85669600	Weak transcription	Colonic Mucosa	Colon
48	chr11:85665200-85742600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr11:85665200-85743000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr11:85665400-85678800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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