Variant report

Variant	rs3766217
Chromosome Location	chr1:47159109-47159110
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47153374..47156939-chr1:47157123..47159935,3	K562	blood:
2	chr1:47157744..47160542-chr1:47181134..47183864,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159658	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10158678	0.94[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs10159351	0.97[EUR][1000 genomes]
rs1025806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1048351	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048380	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1075982	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10890411	0.94[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs11211338	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211341	0.93[EUR][1000 genomes]
rs11211344	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs11211346	0.94[EUR][1000 genomes]
rs1139758	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1150064	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs1150068	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs11801316	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11801419	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11804665	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12047537	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12078635	0.97[EUR][1000 genomes]
rs12082387	0.92[EUR][1000 genomes]
rs12094663	0.94[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1258000	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1258002	0.81[EUR][1000 genomes]
rs1258003	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1258052	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs1258053	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs1258054	0.90[EUR][1000 genomes]
rs1258056	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs1258059	0.90[EUR][1000 genomes]
rs13417	0.94[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs1440485	0.94[CEU][hapmap]
rs1440486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1440489	0.87[EUR][1000 genomes]
rs1440490	0.89[CEU][hapmap]
rs17102352	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17102355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17102428	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs17102473	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1745377	0.94[CEU][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs1933933	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1962900	0.96[EUR][1000 genomes]
rs1971519	0.84[CEU][hapmap]
rs2083486	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs2119301	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2218189	0.94[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs2241862	0.94[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs2289446	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2289447	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2304745	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405026	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2405030	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs34932727	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766211	0.94[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs3766212	0.94[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs3766214	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs3766215	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766219	0.94[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs3766224	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs4272563	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs4274009	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4301586	0.93[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4443838	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55914029	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56319728	0.82[EUR][1000 genomes]
rs58185502	0.93[EUR][1000 genomes]
rs585257	0.94[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs594118	0.93[EUR][1000 genomes]
rs595813	0.93[EUR][1000 genomes]
rs59881815	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60173509	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60675294	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs611468	0.94[CEU][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs614486	0.94[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs61782563	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782568	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61782590	0.86[EUR][1000 genomes]
rs61784001	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61784002	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61784003	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs618554	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs618878	0.80[EUR][1000 genomes]
rs620431	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs620913	0.90[EUR][1000 genomes]
rs625507	0.93[EUR][1000 genomes]
rs625590	0.94[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs637760	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs638845	0.94[EUR][1000 genomes]
rs6429607	0.94[CEU][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs6429608	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6429609	0.86[EUR][1000 genomes]
rs647999	0.94[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs6656244	0.88[ASN][1000 genomes]
rs6666405	0.90[EUR][1000 genomes]
rs6667885	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs6669393	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6670495	0.84[CEU][hapmap]
rs6671005	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6671124	0.94[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs6688195	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs723334	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs723690	0.84[CEU][hapmap]
rs732539	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7354865	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7354894	0.83[CEU][hapmap]
rs7412469	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs744096	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7519866	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532601	0.97[EUR][1000 genomes]
rs7541868	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7553243	0.91[EUR][1000 genomes]
rs8851	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs946320	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3766217	ATPAF1	cis	multi-tissue	Pritchard
rs3766217	MKNK1	cis	cerebellum	SCAN
rs3766217	SLC6A9	cis	parietal	SCAN
rs3766217	FAAH	cis	cerebellum	SCAN
rs3766217	CYP4B1	cis	cerebellum	SCAN
rs3766217	NSUN4	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47138200-47159400	Strong transcription	Placenta	Placenta
2	chr1:47138400-47159400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:47139000-47159400	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:47139200-47159400	Strong transcription	Brain Germinal Matrix	brain
5	chr1:47139200-47159800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:47139400-47159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:47139600-47159400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:47142000-47159400	Strong transcription	K562	blood
10	chr1:47142000-47159800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr1:47142600-47159200	Strong transcription	GM12878-XiMat	blood
12	chr1:47142600-47159400	Strong transcription	NHEK	skin
13	chr1:47142800-47159600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr1:47142800-47159800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:47143200-47159400	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:47143200-47159400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:47143200-47159800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:47143600-47159400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:47143800-47159400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:47143800-47159400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:47143800-47159800	Strong transcription	Primary T cells from cord blood	blood
22	chr1:47143800-47171600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:47144600-47159600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:47148400-47159400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:47148800-47159400	Strong transcription	Hela-S3	cervix
26	chr1:47153200-47159400	Genic enhancers	Fetal Thymus	thymus
27	chr1:47153400-47159600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:47153600-47159400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:47153600-47159600	Strong transcription	Primary hematopoietic stem cells	blood
30	chr1:47154000-47159400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr1:47154000-47159400	Strong transcription	Liver	Liver
32	chr1:47154000-47159800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:47154000-47159800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr1:47154000-47161000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:47154600-47159200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr1:47154600-47183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:47155600-47161000	Weak transcription	Fetal Brain Male	brain
38	chr1:47155600-47169000	Weak transcription	Stomach Mucosa	stomach
39	chr1:47155800-47159400	Strong transcription	HSMM	muscle
40	chr1:47156200-47159400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:47156200-47160800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:47156600-47161000	Weak transcription	NHDF-Ad	bronchial
43	chr1:47157000-47159400	Genic enhancers	Brain Inferior Temporal Lobe	brain
44	chr1:47157200-47159200	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr1:47157200-47159800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:47157200-47159800	Strong transcription	Dnd41	blood
47	chr1:47157200-47161000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:47157400-47159400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
49	chr1:47157400-47159600	Enhancers	Fetal Heart	heart
50	chr1:47157600-47159400	Enhancers	Brain Hippocampus Middle	brain

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