Variant report

Variant	rs11803959
Chromosome Location	chr1:227222125-227222126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10495258	0.94[EUR][1000 genomes]
rs10495263	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs10495266	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10495269	0.94[EUR][1000 genomes]
rs10495270	0.94[EUR][1000 genomes]
rs11799413	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11800062	0.92[EUR][1000 genomes]
rs11801443	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11802395	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11803761	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs11805298	0.81[EUR][1000 genomes]
rs11806820	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11806937	1.00[CEU][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs11807094	0.95[YRI][hapmap]
rs11808186	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11808962	0.94[LWK][hapmap];0.96[YRI][hapmap]
rs11809998	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12401556	0.92[EUR][1000 genomes]
rs12401963	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12403195	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12403391	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12403833	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs12404494	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12404627	0.94[EUR][1000 genomes]
rs12405122	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12405686	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12405707	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12405723	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12405878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12407061	0.94[EUR][1000 genomes]
rs12407545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12408437	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12409816	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12410337	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12410460	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12411017	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1320493	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1513600	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1513603	0.81[EUR][1000 genomes]
rs16846855	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16846874	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16846877	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16846908	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16846910	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16846911	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16846972	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16846985	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16847014	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16847035	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16847098	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16847107	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17605533	0.94[EUR][1000 genomes]
rs17851754	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1877622	1.00[CEU][hapmap];0.81[YRI][hapmap];0.92[EUR][1000 genomes]
rs1888830	0.82[AFR][1000 genomes]
rs1888831	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2090009	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2150869	0.95[EUR][1000 genomes]
rs2150871	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2150873	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2183837	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34400564	0.81[EUR][1000 genomes]
rs34953255	0.94[EUR][1000 genomes]
rs41303115	0.96[EUR][1000 genomes]
rs4551563	0.94[EUR][1000 genomes]
rs55685166	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55865118	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56834719	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57513303	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58532064	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59116340	0.81[EUR][1000 genomes]
rs60079575	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60291100	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60641481	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60866629	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs60979561	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61522132	0.81[EUR][1000 genomes]
rs6675383	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6696791	0.95[EUR][1000 genomes]
rs6696794	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6701743	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73086746	0.92[EUR][1000 genomes]
rs73086752	0.92[EUR][1000 genomes]
rs73086775	0.92[EUR][1000 genomes]
rs73088658	0.81[EUR][1000 genomes]
rs73089725	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73089746	0.83[AFR][1000 genomes]
rs73089747	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73089755	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73089760	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73089765	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73089770	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73090612	0.81[EUR][1000 genomes]
rs73091738	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73091740	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73091742	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73091755	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73091757	0.83[AFR][1000 genomes]
rs73091759	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73091761	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73091766	0.83[AFR][1000 genomes]
rs73091774	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73093463	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73093467	0.82[AFR][1000 genomes]
rs73093495	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73096883	0.81[AFR][1000 genomes]
rs73099023	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73099026	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73100804	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73100814	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73100852	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs73102915	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73102920	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73102930	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73102936	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7413768	0.92[EUR][1000 genomes]
rs74140276	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74140278	0.83[AFR][1000 genomes]
rs74140289	0.81[AFR][1000 genomes]
rs74143321	0.91[EUR][1000 genomes]
rs7535010	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs7539037	0.81[EUR][1000 genomes]
rs7539750	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1007352	chr1:227196502-227247160	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv997751	chr1:227196502-227263537	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1010864	chr1:227199493-227246753	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1014423	chr1:227201253-227268843	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1012482	chr1:227212024-227271750	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11803959	ITPKB	cis	lymphoblastoid	seeQTL
rs11803959	RHOU	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
3	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
4	chr1:227178600-227226200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:227182800-227224200	Weak transcription	Spleen	Spleen
6	chr1:227183200-227228200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:227183200-227240400	Weak transcription	Colonic Mucosa	Colon
8	chr1:227184000-227234000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:227190600-227223200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:227190600-227272600	Weak transcription	Lung	lung
11	chr1:227202600-227222600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:227203000-227278800	Weak transcription	Pancreas	Pancrea
13	chr1:227207600-227242000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:227208800-227222600	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:227209000-227231000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:227209000-227234600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:227209000-227272400	Weak transcription	Fetal Intestine Small	intestine
18	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:227209800-227222800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:227210200-227226400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:227210600-227245800	Weak transcription	NHEK	skin
22	chr1:227212200-227223000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:227212800-227226400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:227213200-227222400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:227213600-227228000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:227214000-227222600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:227214600-227226200	Weak transcription	Brain Germinal Matrix	brain
28	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
29	chr1:227215000-227222400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:227215600-227230400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:227216600-227226400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:227216800-227222400	Weak transcription	Brain Angular Gyrus	brain
33	chr1:227216800-227223000	Strong transcription	HUVEC	blood vessel
34	chr1:227216800-227223200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:227216800-227226200	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:227216800-227226200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:227216800-227231400	Weak transcription	A549	lung
38	chr1:227216800-227235000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:227216800-227239400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:227216800-227287600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:227217000-227226000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:227217000-227226200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr1:227217000-227226200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:227217000-227234000	Weak transcription	Fetal Brain Male	brain
45	chr1:227217000-227264400	Weak transcription	NHLF	lung
46	chr1:227217000-227271400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:227217000-227278800	Weak transcription	Placenta	Placenta
48	chr1:227217200-227241800	Weak transcription	HepG2	liver
49	chr1:227217400-227226400	Weak transcription	HSMMtube	muscle
50	chr1:227218200-227222600	Strong transcription	Adipose Nuclei	Adipose

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