Variant report

Variant	rs1454228
Chromosome Location	chr2:39252554-39252555
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10153761	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10166801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10172085	0.96[EUR][1000 genomes]
rs10184015	0.82[EUR][1000 genomes]
rs10186762	0.89[ASN][1000 genomes]
rs10190377	0.81[EUR][1000 genomes]
rs10192250	0.90[ASN][1000 genomes]
rs10194374	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10439459	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10779924	0.82[ASN][1000 genomes]
rs11124659	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11124660	0.89[EUR][1000 genomes]
rs11692687	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12620071	0.91[EUR][1000 genomes]
rs12712630	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13023273	0.93[ASN][1000 genomes]
rs13031871	0.85[EUR][1000 genomes]
rs13033392	0.81[EUR][1000 genomes]
rs1377860	0.91[EUR][1000 genomes]
rs1377861	0.91[EUR][1000 genomes]
rs1377863	0.91[EUR][1000 genomes]
rs1377864	0.82[EUR][1000 genomes]
rs1454220	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1454221	0.87[ASN][1000 genomes]
rs1454222	0.86[ASN][1000 genomes]
rs1454223	0.92[ASN][1000 genomes]
rs1454225	0.93[ASN][1000 genomes]
rs1454226	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1454227	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1470915	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1840281	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1869513	0.81[ASN][1000 genomes]
rs1947432	0.93[ASN][1000 genomes]
rs2060987	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2060989	0.91[EUR][1000 genomes]
rs2123876	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2123879	0.83[EUR][1000 genomes]
rs2123881	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2168042	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2168044	0.80[ASN][1000 genomes]
rs2278914	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2290445	0.87[ASN][1000 genomes]
rs2373474	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2373495	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2373496	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2888585	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2924714	0.91[EUR][1000 genomes]
rs2969763	0.91[EUR][1000 genomes]
rs297121	0.91[EUR][1000 genomes]
rs297125	0.91[EUR][1000 genomes]
rs297128	0.91[EUR][1000 genomes]
rs297129	0.91[EUR][1000 genomes]
rs297130	0.91[EUR][1000 genomes]
rs297133	0.91[EUR][1000 genomes]
rs297135	0.91[EUR][1000 genomes]
rs297137	0.91[EUR][1000 genomes]
rs297139	0.91[EUR][1000 genomes]
rs297140	0.91[EUR][1000 genomes]
rs297141	0.91[EUR][1000 genomes]
rs297143	0.91[EUR][1000 genomes]
rs297148	0.91[EUR][1000 genomes]
rs297149	0.91[EUR][1000 genomes]
rs297150	0.91[EUR][1000 genomes]
rs297153	0.91[EUR][1000 genomes]
rs297157	0.91[EUR][1000 genomes]
rs297158	0.89[EUR][1000 genomes]
rs297159	0.91[EUR][1000 genomes]
rs378698	0.91[EUR][1000 genomes]
rs4142729	0.92[ASN][1000 genomes]
rs4643520	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4670270	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4670272	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4670903	0.91[ASN][1000 genomes]
rs4670905	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670907	0.86[ASN][1000 genomes]
rs57378308	0.89[EUR][1000 genomes]
rs58645871	0.83[EUR][1000 genomes]
rs59732351	0.89[EUR][1000 genomes]
rs61405040	0.91[EUR][1000 genomes]
rs6544191	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6544194	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6544195	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6544197	0.91[EUR][1000 genomes]
rs6704656	0.82[ASN][1000 genomes]
rs6713281	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6725356	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6725644	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6739568	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6752850	0.91[ASN][1000 genomes]
rs6756184	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72909662	0.89[EUR][1000 genomes]
rs7568552	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7573310	0.82[ASN][1000 genomes]
rs7577088	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7594644	0.81[ASN][1000 genomes]
rs9309031	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs963731	0.87[ASN][1000 genomes]
rs9679498	1.00[AFR][1000 genomes]
rs970409	0.91[EUR][1000 genomes]
rs997344	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1454228	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39213400-39259800	Weak transcription	Right Ventricle	heart
2	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
3	chr2:39219000-39259200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:39227600-39303400	Weak transcription	Colonic Mucosa	Colon
5	chr2:39229800-39293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:39232600-39300000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:39235400-39312000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:39235600-39259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:39235600-39259800	Weak transcription	Spleen	Spleen
10	chr2:39235600-39293200	Weak transcription	Fetal Brain Male	brain
11	chr2:39235600-39295800	Weak transcription	NHLF	lung
12	chr2:39235600-39298200	Weak transcription	Small Intestine	intestine
13	chr2:39235600-39327800	Weak transcription	Esophagus	oesophagus
14	chr2:39235800-39257800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:39235800-39284000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:39235800-39293600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:39236000-39260000	Weak transcription	Hela-S3	cervix
18	chr2:39236000-39295600	Weak transcription	Aorta	Aorta
19	chr2:39236000-39295800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:39236000-39305600	Weak transcription	Gastric	stomach
21	chr2:39236200-39305600	Weak transcription	Lung	lung
22	chr2:39236400-39263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:39237000-39260200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:39237600-39257600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:39238400-39256400	Weak transcription	Fetal Intestine Small	intestine
26	chr2:39238400-39260600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:39238600-39256400	Weak transcription	Fetal Stomach	stomach
28	chr2:39239400-39254600	Weak transcription	Brain Germinal Matrix	brain
29	chr2:39240800-39257600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:39240800-39257800	Weak transcription	Fetal Brain Female	brain
31	chr2:39240800-39262600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:39240800-39299200	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:39241200-39256600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:39241200-39259800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:39241600-39276400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr2:39241600-39292800	Weak transcription	GM12878-XiMat	blood
37	chr2:39243200-39299600	Weak transcription	Brain Substantia Nigra	brain
38	chr2:39244600-39295400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:39244800-39257800	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:39246200-39259600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:39246600-39274000	Weak transcription	Fetal Kidney	kidney
42	chr2:39246800-39254400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:39246800-39257800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:39247600-39252800	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr2:39248000-39257600	Weak transcription	Left Ventricle	heart
46	chr2:39248000-39257800	Weak transcription	HSMMtube	muscle
47	chr2:39248800-39252600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:39249600-39262000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:39250000-39282200	Weak transcription	Brain Anterior Caudate	brain
50	chr2:39250000-39292800	Weak transcription	Psoas Muscle	Psoas

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