Variant report

Variant	rs12486047
Chromosome Location	chr3:56593543-56593544
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10865997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130525	0.81[MEX][hapmap]
rs12496217	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12631156	0.84[AMR][1000 genomes]
rs1316647	0.87[YRI][hapmap]
rs13317989	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs1388256	0.81[MEX][hapmap]
rs2291498	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs282524	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs282525	0.81[MEX][hapmap]
rs282526	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs282530	0.81[MEX][hapmap]
rs282532	0.84[AMR][1000 genomes]
rs282533	0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes]
rs282534	0.82[AMR][1000 genomes]
rs282537	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs282538	0.84[AMR][1000 genomes]
rs282539	0.82[AMR][1000 genomes]
rs282543	0.84[AMR][1000 genomes]
rs35349208	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3732505	0.81[MEX][hapmap]
rs3732513	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4681726	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs4682001	0.82[ASW][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs4974218	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4974222	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4974223	0.81[AMR][1000 genomes]
rs55810735	0.84[EUR][1000 genomes]
rs66873962	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6767903	0.84[YRI][hapmap]
rs6769055	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[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6799711	0.88[AFR][1000 genomes]
rs7612464	0.81[MEX][hapmap]
rs7628343	0.81[AMR][1000 genomes]
rs7639731	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7640995	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7641898	0.91[YRI][hapmap]
rs873840	0.87[YRI][hapmap]
rs9311609	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs953540	0.87[YRI][hapmap]
rs955248	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9822876	0.88[ASW][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9823685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9834064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9847362	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs9867302	0.87[ASW][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.91[YRI][hapmap]
rs9872059	0.81[MEX][hapmap]
rs9873754	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9881152	0.81[AMR][1000 genomes]
rs9985317	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12486047	FLNB	cis	cerebellum	SCAN
rs12486047	C3orf63	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56591800-56596000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:56591800-56599800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:56592000-56615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:56592200-56609400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:56592400-56593600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:56592400-56593600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:56592400-56593800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr3:56592400-56593800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:56592400-56593800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:56592400-56594000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr3:56592400-56594000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:56592400-56594000	Weak transcription	Fetal Thymus	thymus
13	chr3:56592400-56594200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:56592400-56594600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:56592400-56594800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr3:56592400-56594800	Weak transcription	HSMM	muscle
17	chr3:56592400-56596000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:56592400-56596000	Weak transcription	Fetal Stomach	stomach
19	chr3:56592400-56596800	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:56592400-56599800	Weak transcription	Fetal Lung	lung
21	chr3:56592400-56600000	Weak transcription	Ovary	ovary
22	chr3:56592400-56601200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:56592400-56601400	Weak transcription	Left Ventricle	heart
24	chr3:56592400-56601800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:56592400-56601800	Weak transcription	Lung	lung
26	chr3:56592400-56602000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:56592400-56602800	Weak transcription	Esophagus	oesophagus
28	chr3:56592400-56602800	Weak transcription	Gastric	stomach
29	chr3:56592400-56602800	Weak transcription	Spleen	Spleen
30	chr3:56592400-56603000	Weak transcription	Pancreas	Pancrea
31	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
32	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
34	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
35	chr3:56592600-56593600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:56592600-56593600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr3:56592600-56593800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr3:56592600-56593800	Enhancers	Hela-S3	cervix
39	chr3:56592600-56594200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:56592600-56594200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:56592600-56594200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr3:56592600-56594200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:56592600-56594200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:56592600-56594400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:56592600-56594600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:56592600-56594600	Weak transcription	Osteobl	bone
47	chr3:56592600-56594800	Weak transcription	Liver	Liver
48	chr3:56592600-56594800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:56592600-56595600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:56592600-56595800	Weak transcription	Stomach Smooth Muscle	stomach

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