Variant report

Variant	rs3766151
Chromosome Location	chr1:169855576-169855577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169836372..169839147-chr1:169853972..169856036,2	K562	blood:
2	chr1:169812533..169814235-chr1:169854142..169856140,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10733054	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs10737549	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10737550	0.85[ASN][1000 genomes]
rs10737551	0.89[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs10800479	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10800480	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10800481	0.90[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10800483	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10800484	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10800485	0.96[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10800486	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10919239	0.88[ASW][hapmap];0.91[CEU][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap]
rs10919245	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10919248	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10919251	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10919257	0.85[ASN][1000 genomes]
rs10919263	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12133843	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12724797	0.81[MEX][hapmap]
rs1883436	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2056980	0.88[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs2056981	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2179396	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2281039	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2294322	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2294496	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2420512	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2420514	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2491087	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2750016	0.84[CEU][hapmap]
rs2806386	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs2806393	0.84[CEU][hapmap]
rs2901179	0.90[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs3753308	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3766132	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3766134	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3766137	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3766142	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766144	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3766148	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766154	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3917412	0.84[MEX][hapmap]
rs4376791	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4508080	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4614317	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4615900	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4656196	0.91[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4656197	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs4656199	0.86[ASN][1000 genomes]
rs4656200	0.86[ASN][1000 genomes]
rs4656721	0.89[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4656724	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs4656725	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6427217	0.83[JPT][hapmap]
rs6427220	0.83[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs6427224	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6427225	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6427226	0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs6427227	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6427228	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6656965	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6664099	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6668114	0.84[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs6669794	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6670818	0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6671752	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6680508	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs6680650	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6682137	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6682835	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683056	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6684481	0.85[ASN][1000 genomes]
rs6687377	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6702969	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs717481	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs732185	0.95[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7519364	0.84[ASN][1000 genomes]
rs7525259	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7530237	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7545011	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9287097	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][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	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3766151	C1orf112	cis	cerebellum	SCAN
rs3766151	C1orf112	Cis_1M	lymphoblastoid	RTeQTL
rs3766151	SCYL3	Cis_1M	lymphoblastoid	RTeQTL
rs3766151	ANKRD36BP1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
3	chr1:169833800-169860200	Weak transcription	HMEC	breast
4	chr1:169842200-169857400	Weak transcription	Fetal Brain Male	brain
5	chr1:169842400-169855600	Weak transcription	Brain Angular Gyrus	brain
6	chr1:169842400-169860000	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:169844000-169860000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:169844400-169857400	Weak transcription	K562	blood
9	chr1:169844800-169856000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:169844800-169860600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:169845200-169857200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:169845200-169857200	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:169845200-169857400	Weak transcription	HUVEC	blood vessel
14	chr1:169845200-169861400	Weak transcription	Right Ventricle	heart
15	chr1:169845200-169861400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:169845400-169859600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:169845400-169860000	Weak transcription	Psoas Muscle	Psoas
18	chr1:169845400-169861400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:169845800-169855600	Weak transcription	A549	lung
20	chr1:169846000-169858000	Weak transcription	Small Intestine	intestine
21	chr1:169847000-169859000	Weak transcription	Left Ventricle	heart
22	chr1:169847200-169855600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:169847200-169860000	Weak transcription	Brain Substantia Nigra	brain
24	chr1:169847200-169860000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:169847400-169860000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:169848000-169855600	Weak transcription	NH-A	brain
27	chr1:169848000-169859000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:169848000-169860000	Weak transcription	HepG2	liver
29	chr1:169848400-169860600	Weak transcription	Fetal Heart	heart
30	chr1:169848600-169857400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:169848800-169855600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:169848800-169855600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:169848800-169859000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:169850200-169858000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:169850200-169858200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr1:169850600-169858000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr1:169850600-169858200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:169850800-169856000	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:169850800-169858000	Strong transcription	Adipose Nuclei	Adipose
40	chr1:169850800-169858000	Strong transcription	Fetal Intestine Large	intestine
41	chr1:169850800-169858200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:169851200-169857000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:169851600-169858200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:169851600-169859800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:169851600-169861200	Weak transcription	Aorta	Aorta
46	chr1:169851600-169861400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:169851800-169858000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr1:169851800-169860000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:169852000-169860000	Weak transcription	Lung	lung
50	chr1:169852200-169858200	Strong transcription	Rectal Mucosa Donor 29	rectum

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