Variant report

Variant	rs2816193
Chromosome Location	chr1:179139556-179139557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1078872	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs10913690	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10913692	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10913693	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10913695	0.84[ASN][1000 genomes]
rs10913697	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12130276	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs1325195	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1763022	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1807916	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1826183	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1856968	0.82[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1858551	0.86[ASN][1000 genomes]
rs2050923	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2066279	0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2087559	0.94[ASN][1000 genomes]
rs2130576	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2171958	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2171959	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2258221	0.86[ASN][1000 genomes]
rs2306941	0.90[EUR][1000 genomes]
rs2486995	0.86[ASN][1000 genomes]
rs2486997	0.88[ASN][1000 genomes]
rs2486998	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2487563	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2493123	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2493124	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2636272	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2636274	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2636275	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2636276	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2636277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2636278	0.84[GIH][hapmap]
rs2636280	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2636282	0.82[ASN][1000 genomes]
rs2636291	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2636293	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap]
rs2791936	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2791940	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2791941	0.90[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2791942	0.84[ASN][1000 genomes]
rs2791943	0.88[ASN][1000 genomes]
rs2791944	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2791945	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2793790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793793	0.94[ASN][1000 genomes]
rs2793794	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2793795	0.82[ASN][1000 genomes]
rs2793796	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2793797	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2793798	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2793800	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2793801	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2793802	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2793803	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2793810	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2793812	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2793813	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2793816	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs2816166	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2816168	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816183	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2816184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816185	0.90[ASN][1000 genomes]
rs2816186	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs2816187	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2816189	0.93[ASN][1000 genomes]
rs2816190	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];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2816191	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2816196	0.83[ASN][1000 genomes]
rs2816197	0.86[ASN][1000 genomes]
rs2816198	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2816199	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2816200	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2816201	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2816202	0.86[ASN][1000 genomes]
rs2816203	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2816204	0.85[ASN][1000 genomes]
rs2816207	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2816208	0.82[ASN][1000 genomes]
rs2816212	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2816213	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2816214	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2816218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3121198	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3122376	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36122838	0.82[ASN][1000 genomes]
rs3813642	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs3813643	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs3829794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs411266	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs413613	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs451088	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap]
rs4651012	0.83[ASN][1000 genomes]
rs4651013	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs915337	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs9286921	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9425839	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs965401	0.94[ASN][1000 genomes]
rs9662858	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9726961	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs9727252	0.86[ASN][1000 genomes]
rs9728480	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9729129	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9729199	0.82[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2816193	FAM20B	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179117800-179186000	Weak transcription	Fetal Stomach	stomach
2	chr1:179122000-179189400	Weak transcription	Primary B cells from cord blood	blood
3	chr1:179122400-179153000	Weak transcription	Primary T cells from cord blood	blood
4	chr1:179122800-179141600	Weak transcription	Fetal Intestine Large	intestine
5	chr1:179134000-179146600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:179134000-179169000	Weak transcription	Fetal Intestine Small	intestine
7	chr1:179135600-179139600	Enhancers	HSMM	muscle
8	chr1:179136400-179144400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:179136600-179140600	Weak transcription	Psoas Muscle	Psoas
10	chr1:179136800-179146200	Weak transcription	Fetal Heart	heart
11	chr1:179138200-179139600	Enhancers	Hela-S3	cervix
12	chr1:179138200-179144400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:179138400-179139600	Enhancers	A549	lung
14	chr1:179138600-179139800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:179138800-179139600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:179138800-179139600	Enhancers	HMEC	breast
17	chr1:179138800-179139600	Enhancers	NHEK	skin
18	chr1:179138800-179139600	Enhancers	NHLF	lung
19	chr1:179138800-179139800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:179138800-179139800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:179138800-179139800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr1:179139000-179139600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:179139000-179139600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr1:179139000-179139600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:179139000-179139600	Enhancers	Brain Anterior Caudate	brain
26	chr1:179139000-179139600	Enhancers	Brain Hippocampus Middle	brain
27	chr1:179139000-179139600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:179139000-179139600	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr1:179139000-179139800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:179139000-179139800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:179139000-179139800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:179139000-179139800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:179139000-179139800	Enhancers	Left Ventricle	heart
34	chr1:179139200-179139600	Enhancers	HepG2	liver
35	chr1:179139200-179139800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:179139200-179139800	Enhancers	Right Ventricle	heart
37	chr1:179139200-179143800	Weak transcription	Brain Angular Gyrus	brain
38	chr1:179139400-179139600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:179139400-179139600	Enhancers	NH-A	brain
40	chr1:179139400-179139800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:179139400-179139800	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:179139400-179139800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:179139400-179139800	Enhancers	Brain Germinal Matrix	brain
44	chr1:179139400-179140400	Enhancers	NHDF-Ad	bronchial
45	chr1:179139400-179140600	Weak transcription	Gastric	stomach
46	chr1:179139400-179140600	Weak transcription	Spleen	Spleen
47	chr1:179139400-179143600	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr1:179139400-179143800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:179139400-179144200	Weak transcription	Adipose Nuclei	Adipose
50	chr1:179139400-179144200	Weak transcription	Brain Substantia Nigra	brain

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