Variant report

Variant	rs4760296
Chromosome Location	chr12:59992201-59992202
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11609644	0.92[EUR][1000 genomes]
rs11615456	0.92[EUR][1000 genomes]
rs12422902	0.94[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12427190	1.00[CEU][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12580155	0.94[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs12580166	0.85[EUR][1000 genomes]
rs17559098	0.85[EUR][1000 genomes]
rs17640150	0.92[EUR][1000 genomes]
rs17640963	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1874638	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35666255	0.87[EUR][1000 genomes]
rs3935589	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4399358	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4399359	0.93[EUR][1000 genomes]
rs4760295	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4760297	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5026370	0.92[EUR][1000 genomes]
rs61933351	0.91[EUR][1000 genomes]
rs61936271	0.92[EUR][1000 genomes]
rs61936275	0.92[EUR][1000 genomes]
rs61936276	0.92[EUR][1000 genomes]
rs61936294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296400	0.91[EUR][1000 genomes]
rs73109969	0.92[EUR][1000 genomes]
rs7312501	0.87[EUR][1000 genomes]
rs7315308	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7975081	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7979792	0.92[EUR][1000 genomes]
rs908095	0.85[EUR][1000 genomes]
rs954322	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs954323	0.83[AMR][1000 genomes];0.93[EUR][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	esv2762982	chr12:59659871-60000135	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1042271	chr12:59668468-59993468	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1038467	chr12:59680717-59999008	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv541507	chr12:59680717-59999008	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1049084	chr12:59700333-59993468	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv899131	chr12:59942122-60124089	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1048949	chr12:59974039-60041477	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1038100	chr12:59983391-60018745	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4760296	WIBG	cis	cerebellum	SCAN
rs4760296	OR6C4	cis	cerebellum	SCAN
rs4760296	SLC16A7	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59991000-60005000	Weak transcription	Lung	lung
2	chr12:59991200-60004600	Weak transcription	Ovary	ovary
3	chr12:59991400-59992600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
4	chr12:59991400-59992800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:59991400-59992800	Weak transcription	Small Intestine	intestine
6	chr12:59991400-59993400	Weak transcription	Right Ventricle	heart
7	chr12:59991400-59994000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr12:59991400-59994800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr12:59991400-59994800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr12:59991400-59995400	Weak transcription	Psoas Muscle	Psoas
11	chr12:59991400-59998800	Weak transcription	Left Ventricle	heart
12	chr12:59991400-60004600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:59991400-60004600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:59991400-60004600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:59991400-60005000	Weak transcription	Pancreas	Pancrea
16	chr12:59991400-60009400	Weak transcription	Gastric	stomach
17	chr12:59991600-59992400	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr12:59991600-59992400	Weak transcription	Brain Angular Gyrus	brain
19	chr12:59991600-59992600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:59991600-59992600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr12:59991600-59992800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr12:59991600-59992800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:59991600-59992800	Weak transcription	HUVEC	blood vessel
24	chr12:59991600-59994400	Enhancers	Adipose Nuclei	Adipose
25	chr12:59991600-59999000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr12:59991600-60003600	Weak transcription	Fetal Thymus	thymus
27	chr12:59991600-60004400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:59991600-60004600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:59991600-60004600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:59991600-60004600	Weak transcription	Brain Anterior Caudate	brain
31	chr12:59991600-60004800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr12:59991600-60005000	Weak transcription	Thymus	Thymus
33	chr12:59991600-60009400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:59991800-59992400	Enhancers	Hela-S3	cervix
35	chr12:59991800-59992600	Enhancers	Dnd41	blood
36	chr12:59991800-59993400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:59991800-59994200	Genic enhancers	Primary T cells from cord blood	blood
38	chr12:59991800-59995600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:59991800-60004800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:59992000-59992400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:59992000-59992400	Weak transcription	Primary B cells from cord blood	blood
42	chr12:59992000-59992800	Weak transcription	Aorta	Aorta
43	chr12:59992000-59992800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr12:59992000-59992800	Enhancers	GM12878-XiMat	blood
45	chr12:59992000-59994400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr12:59992000-59994600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:59992000-59994800	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr12:59992000-59995400	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr12:59992000-59995800	Weak transcription	Colon Smooth Muscle	Colon
50	chr12:59992000-60004400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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