Variant report

Variant	rs541175
Chromosome Location	chr1:189626447-189626448
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:189625524..189628069-chr1:189701890..189703665,2	MCF-7	breast:
2	chr1:189624367..189627091-chr1:189650312..189652304,2	MCF-7	breast:

Extended variants
information (count: 149 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1033838	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1033839	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1033840	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1033841	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1033842	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10489760	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10733059	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10754243	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10800627	0.83[EUR][1000 genomes]
rs10919556	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10919607	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10922360	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10922362	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10922364	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10922365	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10922443	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079862	0.80[EUR][1000 genomes]
rs12118969	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12127003	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12745556	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1339446	0.82[EUR][1000 genomes]
rs1393499	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1393500	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs155901	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs155902	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs155904	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs155916	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1566679	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1976437	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976438	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2027325	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2038651	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2772317	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2772318	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2789893	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2902583	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs471394	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs472341	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs472988	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs473773	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475821	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475908	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476454	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476884	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs477023	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477876	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs478424	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478740	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs478799	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs480025	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs480055	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs480148	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs481737	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs482865	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486286	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487498	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488657	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494220	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494497	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs496089	0.82[ASN][1000 genomes]
rs501912	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502019	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs502044	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs504384	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs507655	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs509442	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs513328	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs513551	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515441	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515528	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516851	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521299	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521702	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs523337	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524177	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs534795	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs534896	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs537703	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs539147	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs540093	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs544343	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs545162	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs548796	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554431	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554852	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557000	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560227	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560685	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs562347	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs563323	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563883	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563908	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564100	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564871	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565944	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs570816	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs571518	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571656	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs571743	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs572342	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573458	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574992	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575402	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575460	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs576034	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576377	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs577137	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577515	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579032	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579567	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581398	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819063	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs693683	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs695185	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524197	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7532675	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7538568	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv548483	chr1:188802542-189672228	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999435	chr1:188997868-189849121	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1012877	chr1:189035500-189804333	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv872658	chr1:189069537-189675416	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv534452	chr1:189129332-189924389	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv872662	chr1:189211622-189741561	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv872673	chr1:189238665-189731048	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2757763	chr1:189246533-189649328	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2758982	chr1:189246533-189649328	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv872683	chr1:189286816-189748851	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv427863	chr1:189356268-189709137	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1003741	chr1:189447275-189702125	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv535241	chr1:189447275-189702125	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1005794	chr1:189488465-190063923	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv872710	chr1:189512884-189695297	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv1004742	chr1:189526599-189652035	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv872712	chr1:189528943-189731048	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv872714	chr1:189543576-189636292	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv872715	chr1:189543576-189731048	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	nsv1009290	chr1:189554045-189908459	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
21	nsv497885	chr1:189562225-190086077	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv872716	chr1:189568547-189736833	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv1011437	chr1:189579890-189642442	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv872717	chr1:189585380-189748851	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv872718	chr1:189589339-189731048	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	nsv872719	chr1:189602917-189731048	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
27	nsv1012902	chr1:189604612-189642442	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv868954	chr1:189605447-190135265	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
29	nsv1005245	chr1:189606869-189648515	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
30	nsv872720	chr1:189620278-189731048	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
31	nsv872721	chr1:189623964-189731048	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:189626000-189629200	Enhancers	HMEC	breast
2	chr1:189626200-189626800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:189626200-189627000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:189626200-189629400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:189626400-189628200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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