Variant report

Variant	rs3766215
Chromosome Location	chr1:47181022-47181023
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	chr1:47179412..47181950-chr1:47182978..47185076,3	MCF-7	breast:
2	chr1:47132699..47135016-chr1:47178544..47181370,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123472	Chromatin interaction
ENSG00000159658	Chromatin interaction
ENSG00000186118	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10158678	0.94[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs10159351	0.98[EUR][1000 genomes]
rs1025806	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1048351	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1048380	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1075982	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[YRI][hapmap];0.96[EUR][1000 genomes]
rs10890411	0.94[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs11211338	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11211341	0.93[EUR][1000 genomes]
rs11211344	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs11211346	0.94[EUR][1000 genomes]
rs1139758	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1150064	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs1150068	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs11801316	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11801419	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11804665	0.96[EUR][1000 genomes]
rs12047537	0.96[EUR][1000 genomes]
rs12078635	0.98[EUR][1000 genomes]
rs12082387	0.91[EUR][1000 genomes]
rs12094663	0.94[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1258000	0.86[EUR][1000 genomes]
rs1258002	0.81[EUR][1000 genomes]
rs1258003	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1258052	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs1258053	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs1258054	0.91[EUR][1000 genomes]
rs1258056	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs1258059	0.91[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];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1440489	0.86[EUR][1000 genomes]
rs1440490	0.89[CEU][hapmap]
rs17102352	0.96[EUR][1000 genomes]
rs17102355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17102428	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs17102473	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1745377	0.94[CEU][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs1933933	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1962900	0.95[EUR][1000 genomes]
rs1971519	0.84[CEU][hapmap]
rs2083486	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs2119301	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2218189	0.94[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs2241862	0.94[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs2289446	0.96[EUR][1000 genomes]
rs2289447	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2304745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2405026	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2405030	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs34932727	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766211	0.94[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs3766212	0.94[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs3766214	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs3766217	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];0.97[EUR][1000 genomes]
rs4274009	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4301586	0.93[CHB][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4443838	0.96[EUR][1000 genomes]
rs55914029	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56319728	0.82[EUR][1000 genomes]
rs58185502	0.94[EUR][1000 genomes]
rs585257	0.94[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs594118	0.93[EUR][1000 genomes]
rs595813	0.93[EUR][1000 genomes]
rs59881815	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60173509	0.96[EUR][1000 genomes]
rs60675294	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61782564	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61782568	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61782590	0.86[EUR][1000 genomes]
rs61784001	0.96[EUR][1000 genomes]
rs61784002	0.96[EUR][1000 genomes]
rs61784003	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs618554	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs620431	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs620913	0.91[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	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6429609	0.86[EUR][1000 genomes]
rs647999	0.94[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs6656244	0.85[ASN][1000 genomes]
rs6666405	0.91[EUR][1000 genomes]
rs6667885	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs6669393	0.96[EUR][1000 genomes]
rs6670495	0.84[CEU][hapmap]
rs6671005	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6671124	0.94[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs6688195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723334	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs723690	0.84[CEU][hapmap]
rs732539	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7354865	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7354894	0.83[CEU][hapmap]
rs7412469	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs744096	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[EUR][1000 genomes]
rs7519866	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7532601	0.98[EUR][1000 genomes]
rs7541868	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7553243	0.91[EUR][1000 genomes]
rs8851	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs946320	0.91[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3766215	NSUN4	cis	cerebellum	SCAN
rs3766215	ATPAF1	Cis_1M	lymphoblastoid	RTeQTL
rs3766215	KIAA0494	Cis_1M	lymphoblastoid	RTeQTL
rs3766215	FAAH	cis	cerebellum	SCAN
rs3766215	SLC6A9	cis	parietal	SCAN
rs3766215	MKNK1	cis	cerebellum	SCAN
rs3766215	CYP4B1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:47154600-47183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:47159200-47182800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:47160600-47181200	Strong transcription	Dnd41	blood
5	chr1:47160800-47181800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:47160800-47182200	Strong transcription	Primary B cells from cord blood	blood
7	chr1:47160800-47182200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:47160800-47182400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:47160800-47182600	Strong transcription	Placenta	Placenta
10	chr1:47161200-47182200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr1:47161400-47182200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:47161400-47182800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:47164400-47182200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:47164400-47182800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:47164600-47181600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:47165600-47182200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:47166200-47182400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:47166600-47182400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:47166600-47182400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:47166600-47182800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:47166600-47182800	Strong transcription	Fetal Thymus	thymus
22	chr1:47166800-47181800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:47166800-47182200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr1:47166800-47182400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:47166800-47182600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:47166800-47182800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:47167000-47182400	Strong transcription	Fetal Muscle Leg	muscle
28	chr1:47167000-47182800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:47167200-47182600	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:47167400-47182000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:47167600-47183400	Weak transcription	Aorta	Aorta
32	chr1:47171200-47182400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr1:47172000-47181400	Strong transcription	HSMM	muscle
34	chr1:47172200-47183800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr1:47172800-47181200	Weak transcription	Right Ventricle	heart
36	chr1:47173000-47182400	Weak transcription	Small Intestine	intestine
37	chr1:47173200-47181200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:47173200-47181200	Weak transcription	Lung	lung
39	chr1:47173200-47182800	Weak transcription	Fetal Heart	heart
40	chr1:47173200-47182800	Weak transcription	Psoas Muscle	Psoas
41	chr1:47173400-47182400	Weak transcription	Brain Substantia Nigra	brain
42	chr1:47173400-47182600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:47173400-47182600	Weak transcription	Fetal Brain Male	brain
44	chr1:47173800-47181200	Weak transcription	Brain Angular Gyrus	brain
45	chr1:47174400-47182200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:47174600-47182000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:47175000-47181800	Strong transcription	Primary hematopoietic stem cells	blood
48	chr1:47175000-47181800	Strong transcription	Thymus	Thymus
49	chr1:47175000-47182200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:47175000-47182200	Strong transcription	Sigmoid Colon	Sigmoid Colon

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