Variant report

Variant	rs3209531
Chromosome Location	chr14:20754712-20754713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10131909	0.89[CHB][hapmap];0.83[CHD][hapmap];0.91[TSI][hapmap]
rs10138971	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10141905	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10147936	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28789219	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28872178	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7142668	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72671233	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72671237	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9743601	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9743818	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901299	chr14:20191869-20756887	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv1043923	chr14:20338742-21336425	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
3	nsv541970	chr14:20338742-21336425	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
4	nsv1043938	chr14:20427182-20776276	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv541971	chr14:20427182-20776276	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1037160	chr14:20517485-20901811	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
7	nsv541974	chr14:20517485-20901811	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
8	nsv869984	chr14:20732655-20776216	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv1806993	chr14:20743269-20841162	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3209531	CCNB1IP1	cis	parietal	SCAN
rs3209531	OR4K1	cis	cerebellum	SCAN
rs3209531	OR4K5	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:20722600-20755000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr14:20724400-20755200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr14:20731400-20755600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr14:20731400-20757000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr14:20740200-20755200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr14:20741200-20756400	Weak transcription	Gastric	stomach
7	chr14:20741200-20757400	Weak transcription	Right Ventricle	heart
8	chr14:20741400-20755800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr14:20741600-20755200	Weak transcription	Aorta	Aorta
10	chr14:20741600-20755200	Weak transcription	Pancreas	Pancrea
11	chr14:20742400-20756600	Weak transcription	Spleen	Spleen
12	chr14:20742400-20759000	Weak transcription	Colon Smooth Muscle	Colon
13	chr14:20742600-20756400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr14:20742800-20754800	Weak transcription	Adipose Nuclei	Adipose
15	chr14:20742800-20755200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr14:20742800-20755800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr14:20742800-20756600	Weak transcription	Colonic Mucosa	Colon
18	chr14:20742800-20756600	Weak transcription	Lung	lung
19	chr14:20743000-20755200	Weak transcription	Left Ventricle	heart
20	chr14:20743000-20756800	Weak transcription	Osteobl	bone
21	chr14:20743600-20755200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr14:20743600-20761800	Weak transcription	Psoas Muscle	Psoas
23	chr14:20743800-20755200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr14:20743800-20756400	Weak transcription	Thymus	Thymus
25	chr14:20744000-20755400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr14:20744000-20755400	Weak transcription	A549	lung
27	chr14:20744000-20757000	Weak transcription	Brain Substantia Nigra	brain
28	chr14:20744200-20754800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr14:20744200-20756800	Weak transcription	HSMMtube	muscle
30	chr14:20744800-20754800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr14:20744800-20754800	Weak transcription	NHDF-Ad	bronchial
32	chr14:20744800-20755200	Weak transcription	GM12878-XiMat	blood
33	chr14:20745200-20755400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr14:20745200-20756800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr14:20745800-20755800	Weak transcription	NH-A	brain
36	chr14:20746000-20755200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr14:20746200-20755600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:20746200-20763400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr14:20746400-20764000	Weak transcription	Fetal Brain Male	brain
40	chr14:20746600-20759000	Weak transcription	Brain Germinal Matrix	brain
41	chr14:20746600-20773200	Weak transcription	Stomach Mucosa	stomach
42	chr14:20746800-20755000	Weak transcription	Fetal Kidney	kidney
43	chr14:20747000-20754800	Weak transcription	HUVEC	blood vessel
44	chr14:20747000-20755400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr14:20747000-20756800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr14:20747000-20757400	Weak transcription	NHEK	skin
47	chr14:20747200-20759400	Weak transcription	HMEC	breast
48	chr14:20747200-20761800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr14:20747200-20766800	Weak transcription	K562	blood
50	chr14:20747400-20755000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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