Variant report

Variant	rs6541172
Chromosome Location	chr1:221273704-221273705
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10218738	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10218739	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1073166	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10746408	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10779421	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10779422	0.81[EUR][1000 genomes]
rs10863580	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863582	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863584	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863585	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863589	0.86[EUR][1000 genomes]
rs11118645	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11118650	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11118657	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12139572	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568940	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1372665	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1417921	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1442465	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1539139	0.86[EUR][1000 genomes]
rs1867071	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1965817	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1992480	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2378435	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4359036	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4518910	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4532839	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6541171	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6541179	0.84[EUR][1000 genomes]
rs6541180	0.81[EUR][1000 genomes]
rs6656408	0.85[EUR][1000 genomes]
rs6656596	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6657690	0.86[EUR][1000 genomes]
rs6664595	0.81[EUR][1000 genomes]
rs6669742	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6677416	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6694121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6696268	0.87[EUR][1000 genomes]
rs7513152	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7527151	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7527891	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7545437	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs894361	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9431421	0.86[EUR][1000 genomes]
rs9431432	0.81[EUR][1000 genomes]
rs9431436	0.81[EUR][1000 genomes]
rs989463	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv873199	chr1:221136672-221451217	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6541172	C1orf115	cis	lymphoblastoid	seeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221269400-221275000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:221270000-221275600	Enhancers	Adipose Nuclei	Adipose
3	chr1:221270200-221274000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr1:221270200-221276400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:221270200-221276400	Enhancers	NHDF-Ad	bronchial
6	chr1:221270400-221274400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:221270800-221275600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:221270800-221276200	Enhancers	NHLF	lung
9	chr1:221271200-221275600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr1:221271400-221273800	Enhancers	Placenta	Placenta
11	chr1:221271400-221274800	Enhancers	HUVEC	blood vessel
12	chr1:221271400-221275200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:221271400-221275800	Enhancers	Hela-S3	cervix
14	chr1:221271600-221274000	Enhancers	Primary B cells from cord blood	blood
15	chr1:221271600-221274200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr1:221271800-221274400	Enhancers	Primary hematopoietic stem cells	blood
17	chr1:221272000-221276400	Enhancers	Osteobl	bone
18	chr1:221272400-221274600	Weak transcription	NH-A	brain
19	chr1:221272400-221276000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:221272800-221273800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:221273000-221273800	Enhancers	Fetal Muscle Leg	muscle
22	chr1:221273200-221273800	Enhancers	Left Ventricle	heart
23	chr1:221273200-221276400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:221273200-221278600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:221273400-221273800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr1:221273400-221273800	Flanking Active TSS	A549	lung
27	chr1:221273400-221274000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:221273400-221274400	Enhancers	K562	blood
29	chr1:221273400-221275000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:221273400-221275600	Enhancers	Colon Smooth Muscle	Colon
31	chr1:221273600-221273800	Enhancers	Fetal Kidney	kidney
32	chr1:221273600-221274400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:221273600-221274800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:221273600-221275000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:221273600-221275600	Enhancers	Fetal Lung	lung
36	chr1:221273600-221276200	Enhancers	HSMM	muscle
37	chr1:221273600-221276200	Enhancers	HSMMtube	muscle

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