Variant report

Variant	rs1466684
Chromosome Location	chr3:151046308-151046309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:151029737..151031573-chr3:151044175..151046393,2	MCF-7	breast:
2	chr3:151045500..151046403-chr3:151556475..151557090,2	K562	blood:
3	chr3:151021027..151023183-chr3:151044316..151046639,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10935838	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11922647	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1352887	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1388619	0.90[ASN][1000 genomes]
rs1388622	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1388623	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1388624	0.93[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs1388626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1463727	0.84[CEU][hapmap]
rs1472121	0.85[CEU][hapmap]
rs1491978	0.93[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs1491979	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1491980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1491981	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[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1873619	0.85[CEU][hapmap]
rs1873622	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1907637	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs2046934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2141631	1.00[YRI][hapmap]
rs2172249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2242353	0.85[CEU][hapmap]
rs2870517	0.93[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3732762	0.90[ASN][1000 genomes]
rs3732764	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3821667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3971191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3975401	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3975403	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3975404	0.83[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4146770	1.00[ASW][hapmap];0.90[CEU][hapmap];0.86[JPT][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4603933	0.84[CEU][hapmap];0.81[CHD][hapmap];1.00[YRI][hapmap]
rs4679802	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680374	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440731	0.94[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6440732	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6440735	0.85[CEU][hapmap]
rs6440739	0.84[CEU][hapmap]
rs6763983	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6767266	0.85[CEU][hapmap]
rs6769397	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6782212	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6790748	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6803224	0.85[CEU][hapmap]
rs6809388	0.92[JPT][hapmap]
rs6809699	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6809705	0.85[JPT][hapmap]
rs7611328	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7615865	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7616382	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs7620353	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7621876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7623356	0.85[CEU][hapmap]
rs7633362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs937124	0.83[CEU][hapmap]
rs9820422	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];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9849395	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs9863821	1.00[ASW][hapmap];0.85[CEU][hapmap]
rs9863983	0.85[CEU][hapmap]
rs9864095	0.85[CEU][hapmap]
rs9865758	0.85[CEU][hapmap]
rs9877389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9878459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv829757	chr3:151044880-151226442	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1466684	CLRN1	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151038800-151046400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:151044400-151047000	Active TSS	Brain Hippocampus Middle	brain
3	chr3:151045000-151046800	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr3:151045000-151046800	Active TSS	Brain Cingulate Gyrus	brain
5	chr3:151045000-151046800	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr3:151045000-151047200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:151045000-151047200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr3:151045200-151046600	Active TSS	Brain Substantia Nigra	brain
9	chr3:151045200-151046800	Active TSS	Duodenum Mucosa	Duodenum
10	chr3:151045200-151046800	Active TSS	Right Atrium	heart
11	chr3:151045200-151047000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr3:151045200-151047600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:151045400-151046400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:151045400-151046400	Weak transcription	Liver	Liver
15	chr3:151045400-151047400	Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr3:151045400-151047800	Active TSS	Primary monocytes fromperipheralblood	blood
17	chr3:151045600-151046600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:151045600-151046600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:151045600-151047200	Active TSS	Primary T cells from cord blood	blood
20	chr3:151045600-151047800	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr3:151045600-151056600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:151045600-151063600	Weak transcription	Brain Angular Gyrus	brain
23	chr3:151045800-151046400	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr3:151045800-151046800	Enhancers	Hela-S3	cervix
25	chr3:151045800-151046800	Enhancers	NHDF-Ad	bronchial
26	chr3:151046000-151046400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:151046000-151046800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:151046000-151046800	Enhancers	Primary B cells from peripheral blood	blood
29	chr3:151046000-151046800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:151046000-151046800	Active TSS	Fetal Intestine Large	intestine
31	chr3:151046000-151046800	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr3:151046000-151046800	Enhancers	Osteobl	bone
33	chr3:151046200-151046400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr3:151046200-151046600	Flanking Active TSS	A549	lung
35	chr3:151046200-151046600	Flanking Active TSS	HMEC	breast
36	chr3:151046200-151046600	Flanking Active TSS	NHEK	skin
37	chr3:151046200-151046800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:151046200-151046800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr3:151046200-151046800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:151046200-151046800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:151046200-151046800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:151046200-151046800	Active TSS	Brain Anterior Caudate	brain
43	chr3:151046200-151046800	Active TSS	Fetal Muscle Trunk	muscle
44	chr3:151046200-151046800	Flanking Active TSS	Fetal Thymus	thymus
45	chr3:151046200-151046800	Active TSS	Rectal Smooth Muscle	rectum
46	chr3:151046200-151046800	Active TSS	Thymus	Thymus
47	chr3:151046200-151047000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:151046200-151047400	Active TSS	Monocytes-CD14+_RO01746	blood

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