Variant report

Variant	rs1124900
Chromosome Location	chr1:57112222-57112223
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10749708	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10789036	0.81[AFR][1000 genomes]
rs10789038	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10789040	0.82[AFR][1000 genomes]
rs10889006	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10889008	0.85[CEU][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11206872	0.89[ASN][1000 genomes]
rs11206885	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11206886	0.81[EUR][1000 genomes]
rs11206888	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11206889	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11206890	0.85[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11206895	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11804779	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12072057	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12073311	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12078260	0.83[AMR][1000 genomes]
rs12738355	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2064421	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2064422	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2092594	0.83[EUR][1000 genomes]
rs2092595	0.92[CEU][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs2143754	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs2245475	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404718	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2404986	0.89[ASN][1000 genomes]
rs2404987	0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs2404994	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2746338	1.00[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2746339	1.00[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2746345	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2746348	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2746349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2746351	0.85[EUR][1000 genomes]
rs2746353	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2796491	0.87[EUR][1000 genomes]
rs2796492	0.88[EUR][1000 genomes]
rs2796493	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2796495	1.00[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2796496	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2796498	1.00[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2796499	0.88[EUR][1000 genomes]
rs2796506	0.83[EUR][1000 genomes]
rs2796507	0.84[EUR][1000 genomes]
rs2796509	0.96[CEU][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2796511	0.84[EUR][1000 genomes]
rs2796512	0.96[CEU][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2796514	0.84[EUR][1000 genomes]
rs2796517	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2796519	0.85[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2796523	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2796527	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2796534	0.92[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2796541	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4551620	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4584419	0.81[AMR][1000 genomes]
rs59223968	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61772962	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61774285	0.84[ASN][1000 genomes]
rs61774288	0.89[ASN][1000 genomes]
rs6588641	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6588643	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6683935	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs715404	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs715405	1.00[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7415042	0.96[CEU][hapmap];0.95[JPT][hapmap]
rs7419053	0.82[CEU][hapmap]
rs7515414	0.82[CEU][hapmap]
rs7519509	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7547486	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs857147	0.92[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs857148	0.92[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs857150	0.82[EUR][1000 genomes]
rs857155	0.96[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs857156	0.83[EUR][1000 genomes]
rs857159	0.81[EUR][1000 genomes]
rs932447	0.81[CEU][hapmap]
rs963528	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9887940	0.86[AFR][1000 genomes];0.82[AMR][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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3371942	chr1:57109389-57112237	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3402388	chr1:57109989-57112537	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57109800-57112400	Active TSS	Rectal Smooth Muscle	rectum
2	chr1:57109800-57113200	Active TSS	Right Atrium	heart
3	chr1:57109800-57114600	Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr1:57110000-57112400	Active TSS	Brain Anterior Caudate	brain
5	chr1:57110000-57112400	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr1:57110000-57112400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:57110000-57112600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:57110000-57113200	Active TSS	Stomach Smooth Muscle	stomach
9	chr1:57110000-57113400	Active TSS	Right Ventricle	heart
10	chr1:57110200-57112600	Active TSS	Left Ventricle	heart
11	chr1:57110200-57112600	Active TSS	A549	lung
12	chr1:57110200-57113000	Active TSS	Fetal Heart	heart
13	chr1:57110400-57112600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr1:57110600-57112400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
15	chr1:57111400-57113000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:57111600-57112400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
17	chr1:57111800-57112600	Active TSS	Fetal Muscle Trunk	muscle
18	chr1:57111800-57113000	Active TSS	Fetal Kidney	kidney
19	chr1:57111800-57113200	Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr1:57112000-57112400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr1:57112000-57112400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:57112000-57112400	Enhancers	Fetal Brain Male	brain
23	chr1:57112000-57112400	Active TSS	Fetal Muscle Leg	muscle
24	chr1:57112000-57112600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:57112000-57112800	Active TSS	HepG2	liver
26	chr1:57112000-57113000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:57112000-57117400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:57112000-57119800	Weak transcription	HUVEC	blood vessel
29	chr1:57112200-57112400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:57112200-57112600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr1:57112200-57112600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:57112200-57112600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:57112200-57112600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr1:57112200-57112600	Active TSS	Brain Hippocampus Middle	brain
35	chr1:57112200-57112800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:57112200-57112800	Enhancers	Colon Smooth Muscle	Colon
37	chr1:57112200-57112800	Flanking Active TSS	Hela-S3	cervix
38	chr1:57112200-57112800	Active TSS	NHLF	lung
39	chr1:57112200-57113600	Enhancers	Fetal Stomach	stomach

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