Variant report

Variant	rs4768153
Chromosome Location	chr12:47771636-47771637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:47667295..47669429-chr12:47769964..47771855,2	MCF-7	breast:
2	chr12:47766787..47769270-chr12:47771320..47773124,2	K562	blood:
3	chr12:47475106..47477797-chr12:47770687..47773338,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM113B-8	chr12:47770307-47773362	predAs_engstrom06_BG718375_1

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10492010	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10492012	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183851	0.85[ASN][1000 genomes]
rs11183853	0.85[ASN][1000 genomes]
rs11183854	0.85[ASN][1000 genomes]
rs11183855	0.85[ASN][1000 genomes]
rs11183856	0.85[ASN][1000 genomes]
rs11183857	0.85[ASN][1000 genomes]
rs11183858	0.85[ASN][1000 genomes]
rs11183859	0.85[ASN][1000 genomes]
rs11183860	0.85[ASN][1000 genomes]
rs11183862	0.85[ASN][1000 genomes]
rs11183863	0.85[ASN][1000 genomes]
rs11183866	0.85[ASN][1000 genomes]
rs11183871	0.85[ASN][1000 genomes]
rs11183874	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183875	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183877	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183878	1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183879	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183880	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183881	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183882	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183883	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183884	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183885	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183886	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183890	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183891	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11183892	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183893	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183894	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183895	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183896	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183897	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183898	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183900	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183901	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183913	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183916	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183917	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183926	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183928	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183930	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183969	1.00[JPT][hapmap]
rs11561402	0.85[ASN][1000 genomes]
rs12227067	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228708	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809861	0.85[ASN][1000 genomes]
rs12809955	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12810168	0.85[ASN][1000 genomes]
rs12814452	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12817826	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12818155	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12818420	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12827137	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12830961	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12832278	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12832953	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1421356	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1833456	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2040644	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2040645	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2040646	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2040647	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2079026	0.85[ASN][1000 genomes]
rs2079027	0.90[ASN][1000 genomes]
rs2079028	0.90[ASN][1000 genomes]
rs215340	1.00[CHD][hapmap]
rs34187987	0.85[ASN][1000 genomes]
rs34692456	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34762197	0.85[ASN][1000 genomes]
rs34878892	0.85[ASN][1000 genomes]
rs35743720	0.85[ASN][1000 genomes]
rs35839210	0.85[ASN][1000 genomes]
rs35889007	0.95[ASN][1000 genomes]
rs36059508	0.85[ASN][1000 genomes]
rs4473016	0.85[ASN][1000 genomes]
rs4768145	0.85[ASN][1000 genomes]
rs4768146	0.85[ASN][1000 genomes]
rs4768147	0.85[ASN][1000 genomes]
rs4768798	0.85[ASN][1000 genomes]
rs4768800	0.85[ASN][1000 genomes]
rs4768805	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs71445736	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4768153	YAF2	cis	parietal	SCAN
rs4768153	TUBA1B	cis	cerebellum	SCAN
rs4768153	RHEBL1	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47762800-47771800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr12:47763200-47772200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:47763200-47772200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:47766600-47772200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr12:47770400-47773200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr12:47770600-47772400	Enhancers	Rectal Smooth Muscle	rectum
7	chr12:47770600-47773200	Enhancers	Adipose Nuclei	Adipose
8	chr12:47770600-47773400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr12:47770800-47771800	Enhancers	Lung	lung
10	chr12:47770800-47771800	Enhancers	NHDF-Ad	bronchial
11	chr12:47770800-47772200	Enhancers	Brain Hippocampus Middle	brain
12	chr12:47770800-47772200	Enhancers	Right Atrium	heart
13	chr12:47770800-47772400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr12:47770800-47772400	Enhancers	Ovary	ovary
15	chr12:47770800-47773400	Enhancers	Liver	Liver
16	chr12:47770800-47773600	Enhancers	HUVEC	blood vessel
17	chr12:47771000-47772000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:47771000-47772200	Enhancers	HMEC	breast
19	chr12:47771000-47772400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:47771000-47772400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:47771000-47772800	Enhancers	NH-A	brain
22	chr12:47771200-47771800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:47771200-47771800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:47771200-47771800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:47771200-47771800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr12:47771200-47771800	Active TSS	Stomach Smooth Muscle	stomach
27	chr12:47771200-47771800	Flanking Active TSS	NHEK	skin
28	chr12:47771200-47772000	Enhancers	Fetal Heart	heart
29	chr12:47771200-47772200	Flanking Active TSS	A549	lung
30	chr12:47771200-47772400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:47771200-47772400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:47771200-47773000	Enhancers	HSMM	muscle
33	chr12:47771200-47773200	Enhancers	Hela-S3	cervix
34	chr12:47771200-47773600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr12:47771400-47771800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:47771400-47771800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:47771400-47771800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:47771400-47771800	Enhancers	Left Ventricle	heart
39	chr12:47771400-47771800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr12:47771400-47771800	Flanking Active TSS	K562	blood
41	chr12:47771400-47771800	Active TSS	NHLF	lung
42	chr12:47771400-47772000	Enhancers	Fetal Muscle Leg	muscle
43	chr12:47771400-47772200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:47771400-47772200	Enhancers	Brain Substantia Nigra	brain
45	chr12:47771400-47772400	Enhancers	Placenta	Placenta
46	chr12:47771600-47771800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:47771600-47771800	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr12:47771600-47771800	Active TSS	Brain Cingulate Gyrus	brain
49	chr12:47771600-47771800	Flanking Active TSS	HSMMtube	muscle
50	chr12:47771600-47772000	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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