Variant report

Variant	rs55949630
Chromosome Location	chr1:171288630-171288631
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10399602	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10399952	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798297	0.91[AMR][1000 genomes]
rs10912672	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10912673	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10912713	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912714	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912723	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10912736	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1126692	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11484641	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11484642	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11487396	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12057955	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12058402	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12059179	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062692	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068552	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12070766	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12072043	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12077231	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12077755	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079141	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12080449	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12081291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091482	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12092985	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094878	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12141555	0.89[AMR][1000 genomes]
rs12354390	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726624	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12729885	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12730181	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12742008	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12745080	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747080	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757839	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13376631	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16864302	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16864387	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2006986	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076322	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2092311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284131	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28741369	0.85[ASN][1000 genomes]
rs34118031	0.85[ASN][1000 genomes]
rs34320519	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4607925	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6424932	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6670639	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6674596	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742350	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs742351	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7512853	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519999	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539057	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541377	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55949630	FMO4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171283600-171293000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:171283600-171297800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:171283800-171289000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:171283800-171291000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:171283800-171292600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:171283800-171293000	Weak transcription	Brain Substantia Nigra	brain
7	chr1:171284000-171289000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:171284000-171290200	Weak transcription	Colonic Mucosa	Colon
9	chr1:171284000-171291200	Weak transcription	Brain Anterior Caudate	brain
10	chr1:171284000-171292800	Weak transcription	Psoas Muscle	Psoas
11	chr1:171284000-171294600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:171284000-171295200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:171284000-171295400	Weak transcription	Stomach Mucosa	stomach
14	chr1:171284000-171312200	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:171284200-171291000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:171284200-171291400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:171284200-171294400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:171284200-171294600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:171284200-171295400	Weak transcription	Esophagus	oesophagus
20	chr1:171284200-171295800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:171284200-171307400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr1:171284200-171313600	Weak transcription	Right Ventricle	heart
23	chr1:171284200-171313800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:171284600-171292400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:171284800-171289000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:171286400-171289000	Weak transcription	Pancreas	Pancrea
27	chr1:171286800-171309200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:171288000-171288800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
29	chr1:171288000-171288800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:171288000-171288800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:171288000-171289200	ZNF genes & repeats	Ovary	ovary
32	chr1:171288000-171289400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:171288000-171289400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr1:171288000-171289600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:171288000-171289800	Strong transcription	Aorta	Aorta
36	chr1:171288000-171289800	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:171288000-171289800	Strong transcription	Left Ventricle	heart
38	chr1:171288000-171290000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:171288200-171288800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
40	chr1:171288200-171289400	Strong transcription	Fetal Lung	lung
41	chr1:171288200-171289800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:171288200-171293800	Strong transcription	Liver	Liver
43	chr1:171288400-171289200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:171288400-171289800	Strong transcription	Primary T cells from cord blood	blood
45	chr1:171288400-171289800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:171288400-171313000	Weak transcription	Gastric	stomach
47	chr1:171288600-171288800	Weak transcription	Lung	lung
48	chr1:171288600-171289400	Strong transcription	Primary B cells from cord blood	blood
49	chr1:171288600-171289400	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr1:171288600-171289600	Strong transcription	Primary hematopoietic stem cells	blood

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