Variant report

Variant	rs11648228
Chromosome Location	chr16:12181702-12181703
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11075049	0.94[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11075054	0.81[ASN][1000 genomes]
rs11639701	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11642033	0.85[ASN][1000 genomes]
rs11642386	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11646458	0.88[ASN][1000 genomes]
rs11646539	0.81[ASN][1000 genomes]
rs11646584	0.85[ASN][1000 genomes]
rs11647572	0.82[ASN][1000 genomes]
rs11648468	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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11648816	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12596549	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12596703	0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12599090	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12599793	0.81[ASN][1000 genomes]
rs12708746	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12708747	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs12926900	0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[ASN][1000 genomes]
rs12929519	0.85[ASN][1000 genomes]
rs13333662	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs13336687	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958964	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175020	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs2457193	0.86[ASN][1000 genomes]
rs28439695	0.87[ASN][1000 genomes]
rs28667047	0.86[ASN][1000 genomes]
rs2869808	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs350233	0.82[JPT][hapmap]
rs350264	0.86[ASN][1000 genomes]
rs350265	0.82[ASN][1000 genomes]
rs350266	0.82[ASN][1000 genomes]
rs35053871	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35318501	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35542345	0.85[ASN][1000 genomes]
rs3851011	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851012	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs3894905	0.83[CHD][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap]
rs4780411	0.98[ASN][1000 genomes]
rs4781180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs71385189	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195019	0.84[AMR][1000 genomes]
rs7200307	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8048589	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050180	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs8055516	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8059989	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8062015	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8063329	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925009	0.94[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9935284	0.81[ASN][1000 genomes]
rs9936270	0.80[ASN][1000 genomes]
rs9939383	0.94[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv977111	chr16:12161129-12220593	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1039492	chr16:12176517-12210702	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv571460	chr16:12181702-12238602	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11648228	TNFRSF17	cis	cerebellum	SCAN
rs11648228	MYH11	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12117400-12183400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr16:12142800-12189200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr16:12146000-12183400	Weak transcription	Fetal Intestine Large	intestine
4	chr16:12148000-12183400	Weak transcription	Fetal Lung	lung
5	chr16:12156000-12185800	Weak transcription	Brain Germinal Matrix	brain
6	chr16:12156000-12185800	Weak transcription	Fetal Brain Female	brain
7	chr16:12157000-12181800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr16:12157200-12183200	Weak transcription	NHLF	lung
9	chr16:12157200-12185800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr16:12157800-12185800	Weak transcription	HSMMtube	muscle
11	chr16:12163600-12183600	Weak transcription	Colon Smooth Muscle	Colon
12	chr16:12167600-12185800	Weak transcription	HSMM	muscle
13	chr16:12170000-12183400	Weak transcription	HepG2	liver
14	chr16:12170200-12183400	Weak transcription	Colonic Mucosa	Colon
15	chr16:12170600-12182000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr16:12173400-12183200	Weak transcription	Liver	Liver
17	chr16:12173600-12182800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr16:12173600-12183400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr16:12173600-12183400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr16:12173800-12183200	Weak transcription	Brain Hippocampus Middle	brain
21	chr16:12173800-12183400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr16:12173800-12183400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr16:12174200-12181800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr16:12174200-12183000	Weak transcription	HUVEC	blood vessel
25	chr16:12174200-12183200	Weak transcription	Osteobl	bone
26	chr16:12174200-12183400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr16:12174400-12182000	Weak transcription	Spleen	Spleen
28	chr16:12174400-12182400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr16:12174400-12183200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr16:12175000-12181800	Weak transcription	Brain Anterior Caudate	brain
31	chr16:12175200-12185000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr16:12175400-12183200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr16:12175600-12183200	Weak transcription	Fetal Intestine Small	intestine
34	chr16:12175600-12183400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr16:12175800-12183200	Weak transcription	NH-A	brain
36	chr16:12176000-12181800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr16:12176000-12181800	Weak transcription	Fetal Muscle Leg	muscle
38	chr16:12176000-12183400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr16:12176200-12183200	Weak transcription	Fetal Kidney	kidney
40	chr16:12176200-12183200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr16:12176400-12183200	Weak transcription	NHDF-Ad	bronchial
42	chr16:12176400-12183400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr16:12176600-12183400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr16:12176800-12181800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr16:12176800-12181800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr16:12176800-12183000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr16:12177600-12183000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr16:12177800-12182800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr16:12177800-12182800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr16:12177800-12182800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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