Variant report

Variant	rs60249173
Chromosome Location	chr3:143559661-143559662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143552824..143555742-chr3:143557678..143559714,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10513218	0.81[ASN][1000 genomes]
rs1394398	0.85[ASN][1000 genomes]
rs1504603	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1504604	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1995529	0.85[ASN][1000 genomes]
rs1995530	0.85[ASN][1000 genomes]
rs2011303	0.85[ASN][1000 genomes]
rs2361205	1.00[ASN][1000 genomes]
rs2885195	0.85[ASN][1000 genomes]
rs4499594	0.85[ASN][1000 genomes]
rs56124843	0.81[ASN][1000 genomes]
rs56220620	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56407400	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57262535	0.81[ASN][1000 genomes]
rs57718888	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58621433	0.81[ASN][1000 genomes]
rs58887384	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58921154	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59306133	0.85[ASN][1000 genomes]
rs59653678	0.81[ASN][1000 genomes]
rs60523819	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60550983	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6762196	0.81[ASN][1000 genomes]
rs6768399	0.81[ASN][1000 genomes]
rs6794907	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73869037	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73869039	1.00[ASN][1000 genomes]
rs73869041	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73869042	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73869048	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73869049	0.85[ASN][1000 genomes]
rs73869050	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73871822	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73871823	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73871826	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73871827	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73871828	1.00[AMR][1000 genomes]
rs7434217	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7613146	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7637640	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7653164	0.81[ASN][1000 genomes]
rs9824974	0.85[ASN][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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143541400-143565200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:143545600-143565400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:143549200-143565200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:143549400-143565000	Weak transcription	Primary T cells from cord blood	blood
5	chr3:143550000-143565200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:143551400-143561600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:143551400-143563000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:143551400-143565800	Weak transcription	Adipose Nuclei	Adipose
9	chr3:143551600-143559800	Weak transcription	Stomach Mucosa	stomach
10	chr3:143551800-143563600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:143554200-143565800	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:143555400-143564200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:143556400-143560200	Enhancers	Colon Smooth Muscle	Colon
14	chr3:143556800-143563800	Weak transcription	Brain Angular Gyrus	brain
15	chr3:143557800-143560200	Enhancers	Brain Substantia Nigra	brain
16	chr3:143558000-143560000	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr3:143558000-143560200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:143558000-143560200	Enhancers	Rectal Smooth Muscle	rectum
19	chr3:143558200-143559800	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr3:143558200-143560200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:143558200-143560200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:143558200-143560200	Enhancers	Fetal Lung	lung
23	chr3:143558400-143559800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr3:143558400-143559800	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr3:143558400-143561600	Weak transcription	Brain Anterior Caudate	brain
26	chr3:143558400-143563800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:143558400-143566600	Weak transcription	Esophagus	oesophagus
28	chr3:143558600-143561200	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:143558600-143566000	Weak transcription	Ovary	ovary
30	chr3:143558800-143559800	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr3:143558800-143560200	Enhancers	Primary B cells from peripheral blood	blood
32	chr3:143558800-143560200	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr3:143559000-143559800	Enhancers	Primary B cells from cord blood	blood
34	chr3:143559000-143560200	Enhancers	Brain Cingulate Gyrus	brain
35	chr3:143559000-143561600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:143559200-143559800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr3:143559200-143560000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:143559400-143560200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:143559600-143560200	Enhancers	Small Intestine	intestine
40	chr3:143559600-143560200	Enhancers	GM12878-XiMat	blood
41	chr3:143559600-143562400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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