Variant report

Variant	rs55660948
Chromosome Location	chr1:180409384-180409385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10494528	0.93[EUR][1000 genomes]
rs10494529	0.93[EUR][1000 genomes]
rs1069436	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913988	0.93[EUR][1000 genomes]
rs10913990	0.89[EUR][1000 genomes]
rs10913991	0.93[EUR][1000 genomes]
rs10913992	0.93[EUR][1000 genomes]
rs10913995	0.91[EUR][1000 genomes]
rs10913996	0.93[EUR][1000 genomes]
rs10914004	0.93[EUR][1000 genomes]
rs10914012	0.83[EUR][1000 genomes]
rs11487431	0.93[EUR][1000 genomes]
rs12058221	0.83[EUR][1000 genomes]
rs12062561	0.83[EUR][1000 genomes]
rs12065388	0.88[EUR][1000 genomes]
rs12069389	0.83[EUR][1000 genomes]
rs12070624	0.93[EUR][1000 genomes]
rs12071353	0.93[EUR][1000 genomes]
rs12076995	0.93[EUR][1000 genomes]
rs12077656	0.93[EUR][1000 genomes]
rs12077791	0.83[EUR][1000 genomes]
rs12077839	0.83[EUR][1000 genomes]
rs12081494	0.91[EUR][1000 genomes]
rs12083900	0.93[EUR][1000 genomes]
rs12084039	0.93[EUR][1000 genomes]
rs12087060	0.88[EUR][1000 genomes]
rs12087325	0.93[EUR][1000 genomes]
rs12089373	0.81[EUR][1000 genomes]
rs12093073	0.83[EUR][1000 genomes]
rs1339721	0.83[EUR][1000 genomes]
rs16856042	0.88[EUR][1000 genomes]
rs2254465	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764433	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764450	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs357047	0.87[ASN][1000 genomes]
rs4403592	0.93[EUR][1000 genomes]
rs55912749	0.80[EUR][1000 genomes]
rs55962675	0.93[EUR][1000 genomes]
rs56079047	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56303477	0.89[EUR][1000 genomes]
rs56333717	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56747078	0.88[EUR][1000 genomes]
rs57070632	0.88[EUR][1000 genomes]
rs57424497	0.93[EUR][1000 genomes]
rs57493263	0.93[EUR][1000 genomes]
rs58145394	0.90[EUR][1000 genomes]
rs58369506	0.93[EUR][1000 genomes]
rs59357483	0.93[EUR][1000 genomes]
rs59371134	0.88[EUR][1000 genomes]
rs60528279	0.88[EUR][1000 genomes]
rs61024380	0.93[EUR][1000 genomes]
rs6425635	0.93[EUR][1000 genomes]
rs6659477	0.89[EUR][1000 genomes]
rs66619942	0.93[EUR][1000 genomes]
rs6663823	0.93[EUR][1000 genomes]
rs6667388	0.93[EUR][1000 genomes]
rs6670242	0.93[EUR][1000 genomes]
rs6670868	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673113	0.88[EUR][1000 genomes]
rs6676778	0.93[EUR][1000 genomes]
rs66913400	0.93[EUR][1000 genomes]
rs6696075	0.93[EUR][1000 genomes]
rs67071426	0.93[EUR][1000 genomes]
rs67343454	0.88[EUR][1000 genomes]
rs67517246	0.88[EUR][1000 genomes]
rs67621570	0.93[EUR][1000 genomes]
rs67623108	0.88[EUR][1000 genomes]
rs67716213	0.93[EUR][1000 genomes]
rs67830766	0.93[EUR][1000 genomes]
rs68010689	0.88[EUR][1000 genomes]
rs68046305	0.86[EUR][1000 genomes]
rs72714809	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714814	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714815	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714816	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72714819	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714820	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714824	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714859	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714872	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714883	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714890	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714891	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714892	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714896	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72716605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72716619	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72716624	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72716634	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72716637	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72720921	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72720928	0.80[EUR][1000 genomes]
rs72720930	0.80[EUR][1000 genomes]
rs73037411	0.93[EUR][1000 genomes]
rs73048237	0.93[EUR][1000 genomes]
rs7533389	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542223	0.93[EUR][1000 genomes]
rs7552701	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9662762	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv527918	chr1:180279710-180443808	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
6	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
7	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180365200-180420600	Weak transcription	A549	lung
2	chr1:180379000-180430800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:180382400-180410800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:180389800-180410400	Weak transcription	Fetal Intestine Large	intestine
5	chr1:180391200-180410200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:180392600-180446200	Weak transcription	K562	blood
7	chr1:180394800-180420200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:180399000-180420800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:180399600-180420400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:180399600-180420400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:180401400-180413800	Weak transcription	Small Intestine	intestine
12	chr1:180401400-180420200	Weak transcription	HSMM	muscle
13	chr1:180401400-180430400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:180401800-180410200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:180401800-180420800	Weak transcription	NHDF-Ad	bronchial
16	chr1:180402400-180411400	Weak transcription	Spleen	Spleen
17	chr1:180403400-180410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:180403400-180426200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:180403400-180431200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:180403400-180448000	Weak transcription	HMEC	breast
21	chr1:180404000-180421800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:180404200-180431800	Weak transcription	NHEK	skin
23	chr1:180404400-180469000	Weak transcription	Pancreas	Pancrea
24	chr1:180406200-180420200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:180406600-180409600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:180406600-180420600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:180406800-180410000	Weak transcription	Dnd41	blood
28	chr1:180407600-180411200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:180408400-180410200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:180408400-180411000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:180408600-180412400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:180409000-180409600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:180409200-180409800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
34	chr1:180409200-180421200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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