Variant report

Variant	rs4845513
Chromosome Location	chr1:152998066-152998067
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	chr1:152997979..153000273-chr1:153001489..153003586,2	MCF-7	breast:
2	chr1:152997652..153000617-chr1:153004018..153006664,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169469	Chromatin interaction

Extended variants
information (count: 266 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:257)

rs_ID	r²[population]
rs1015995	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs1015996	0.80[ASN][1000 genomes]
rs1048296	0.90[CHB][hapmap];0.97[ASN][1000 genomes]
rs10494285	0.82[ASN][1000 genomes]
rs1055935	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs10788850	0.91[CHB][hapmap]
rs10788852	0.99[ASN][1000 genomes]
rs10788853	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs10788854	0.97[ASN][1000 genomes]
rs10788855	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs10788856	0.97[ASN][1000 genomes]
rs10788857	0.82[ASN][1000 genomes]
rs10888523	0.82[ASN][1000 genomes]
rs10888524	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10888525	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs10888526	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs10888527	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs10888528	0.80[CEU][hapmap];0.92[EUR][1000 genomes]
rs10888529	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs1108410	0.96[CEU][hapmap];0.99[EUR][1000 genomes]
rs11205164	0.84[ASN][1000 genomes]
rs11205165	0.84[ASN][1000 genomes]
rs11205166	0.96[ASN][1000 genomes]
rs11205172	0.84[ASN][1000 genomes]
rs11205174	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs11205175	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs11205176	0.86[ASN][1000 genomes]
rs11205177	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs11205179	0.98[EUR][1000 genomes]
rs11205180	0.98[EUR][1000 genomes]
rs11205181	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs11205182	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs11205186	0.85[EUR][1000 genomes]
rs11205187	0.91[EUR][1000 genomes]
rs11205188	0.91[EUR][1000 genomes]
rs11205189	0.91[EUR][1000 genomes]
rs1129655	0.91[CHB][hapmap]
rs1134220	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs11485498	0.94[EUR][1000 genomes]
rs11488175	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs11576797	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs11590835	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs11812015	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs12029168	0.84[ASN][1000 genomes]
rs12079087	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs12082627	0.98[EUR][1000 genomes]
rs12083211	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs12085426	0.86[ASN][1000 genomes]
rs12195	0.96[ASN][1000 genomes]
rs1334848	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs1334849	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs1334850	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs1338178	0.82[ASN][1000 genomes]
rs1338180	0.82[ASN][1000 genomes]
rs1338181	0.96[ASN][1000 genomes]
rs1413848	0.91[CHB][hapmap]
rs1413849	0.91[CHB][hapmap]
rs1415959	0.91[CHB][hapmap]
rs1415960	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1415961	0.91[CHB][hapmap]
rs1415965	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs1415966	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs1415968	0.91[CHB][hapmap]
rs1415969	0.97[ASN][1000 genomes]
rs1415972	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs1500937	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs1577960	0.98[EUR][1000 genomes]
rs1591736	0.84[ASN][1000 genomes]
rs1611753	0.91[CHB][hapmap]
rs1611754	0.84[ASN][1000 genomes]
rs1611759	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1611760	0.91[CHB][hapmap]
rs1611762	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1611764	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1750309	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs1890285	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs1933381	0.86[ASN][1000 genomes]
rs1933382	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs1933383	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs1970328	0.80[ASN][1000 genomes]
rs1984197	0.91[CHB][hapmap]
rs1995308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1999886	0.91[CHB][hapmap]
rs2050673	0.81[CEU][hapmap]
rs2070963	0.97[ASN][1000 genomes]
rs2070964	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs2152993	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs2152994	0.84[ASN][1000 genomes]
rs2225919	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2339489	0.80[ASN][1000 genomes]
rs2339490	0.83[ASN][1000 genomes]
rs2339491	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs2339492	0.84[ASN][1000 genomes]
rs2339493	0.91[CHB][hapmap]
rs2339495	0.91[CHB][hapmap]
rs2339496	0.86[ASN][1000 genomes]
rs2651413	0.97[ASN][1000 genomes]
rs2711	0.97[ASN][1000 genomes]
rs2787629	0.97[ASN][1000 genomes]
rs2879487	0.84[ASN][1000 genomes]
rs2879489	0.91[CHB][hapmap]
rs28924721	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs310103	0.95[CHB][hapmap]
rs310105	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs310109	0.85[CHB][hapmap]
rs310124	0.83[ASN][1000 genomes]
rs310126	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs3120744	0.96[ASN][1000 genomes]
rs3170863	0.91[CHB][hapmap]
rs3181787	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs368912	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs370162	0.97[ASN][1000 genomes]
rs372490	0.97[ASN][1000 genomes]
rs3737864	0.92[EUR][1000 genomes]
rs3737867	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs3753454	0.91[CHB][hapmap]
rs377768	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs3795381	0.97[ASN][1000 genomes]
rs3795382	0.97[ASN][1000 genomes]
rs3806219	0.91[CHB][hapmap]
rs3806221	0.86[ASN][1000 genomes]
rs3806222	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs3806223	0.86[ASN][1000 genomes]
rs3820141	0.97[ASN][1000 genomes]
rs382653	0.97[ASN][1000 genomes]
rs387930	0.91[CHB][hapmap]
rs394859	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs399550	0.91[CHB][hapmap]
rs4041401	0.84[ASN][1000 genomes]
rs406350	0.97[ASN][1000 genomes]
rs407103	0.97[ASN][1000 genomes]
rs407448	0.83[ASN][1000 genomes]
rs409986	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs41263664	0.84[EUR][1000 genomes]
rs419721	0.97[ASN][1000 genomes]
rs423692	0.97[ASN][1000 genomes]
rs4240865	0.91[CHB][hapmap]
rs4240866	0.90[CHB][hapmap]
rs4240867	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4240868	0.82[ASN][1000 genomes]
rs426360	0.83[ASN][1000 genomes]
rs427470	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs431242	0.95[CHB][hapmap]
rs4314835	0.84[ASN][1000 genomes]
rs4323653	0.82[ASN][1000 genomes]
rs435633	0.97[ASN][1000 genomes]
rs4363385	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs436621	0.97[ASN][1000 genomes]
rs440598	0.91[CHB][hapmap]
rs441229	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs4452994	0.84[ASN][1000 genomes]
rs4478766	0.84[ASN][1000 genomes]
rs451939	0.97[ASN][1000 genomes]
rs454245	0.91[CHB][hapmap]
rs454993	0.97[ASN][1000 genomes]
rs4576617	0.84[ASN][1000 genomes]
rs472076	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs4845331	0.82[ASN][1000 genomes]
rs4845332	0.82[ASN][1000 genomes]
rs4845333	0.82[ASN][1000 genomes]
rs4845334	0.82[ASN][1000 genomes]
rs4845335	0.84[ASN][1000 genomes]
rs4845336	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs4845503	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845505	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845509	0.82[ASN][1000 genomes]
rs4845511	0.84[ASN][1000 genomes]
rs4845512	0.99[ASN][1000 genomes]
rs4845514	0.91[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4845515	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs4845518	0.80[CEU][hapmap];0.82[ASN][1000 genomes]
rs4845519	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs4845522	0.97[ASN][1000 genomes]
rs489323	0.97[ASN][1000 genomes]
rs512198	0.97[ASN][1000 genomes]
rs529077	0.97[ASN][1000 genomes]
rs532743	0.97[ASN][1000 genomes]
rs532773	0.97[ASN][1000 genomes]
rs546666	0.83[ASN][1000 genomes]
rs557553	0.96[ASN][1000 genomes]
rs558363	0.97[ASN][1000 genomes]
rs55906223	0.90[EUR][1000 genomes]
rs559236	0.97[ASN][1000 genomes]
rs561143	0.97[ASN][1000 genomes]
rs56158137	0.99[EUR][1000 genomes]
rs56412380	0.99[EUR][1000 genomes]
rs572821	0.97[ASN][1000 genomes]
rs574649	0.97[ASN][1000 genomes]
rs576941	0.91[CHB][hapmap]
rs581447	0.91[CHB][hapmap]
rs582345	0.91[CHB][hapmap]
rs608509	0.91[CHB][hapmap]
rs61811862	0.99[ASN][1000 genomes]
rs61811863	0.87[ASN][1000 genomes]
rs61811886	0.94[EUR][1000 genomes]
rs61811902	0.91[EUR][1000 genomes]
rs61811903	0.92[EUR][1000 genomes]
rs653332	0.97[ASN][1000 genomes]
rs6587717	0.82[ASN][1000 genomes]
rs6587719	0.84[ASN][1000 genomes]
rs6587724	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs6587725	0.92[EUR][1000 genomes]
rs662506	0.91[CHB][hapmap]
rs6660797	0.94[EUR][1000 genomes]
rs6660878	0.97[EUR][1000 genomes]
rs6661059	0.97[EUR][1000 genomes]
rs6661063	0.94[EUR][1000 genomes]
rs6661791	0.87[ASN][1000 genomes]
rs6664380	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs6664823	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs6667418	0.91[CHB][hapmap]
rs6668311	0.91[CHB][hapmap]
rs6670380	0.93[EUR][1000 genomes]
rs6670614	0.91[CHB][hapmap]
rs6671414	0.91[CHB][hapmap]
rs6671524	0.91[CHB][hapmap]
rs6672735	0.82[ASN][1000 genomes]
rs6673356	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs6675009	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs6677674	0.92[EUR][1000 genomes]
rs6679201	0.82[ASN][1000 genomes]
rs6680061	0.94[EUR][1000 genomes]
rs6680624	0.83[ASN][1000 genomes]
rs6683514	0.87[EUR][1000 genomes]
rs6684188	0.91[CHB][hapmap]
rs6685731	0.83[ASN][1000 genomes]
rs6686526	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs6689066	0.93[EUR][1000 genomes]
rs6689510	0.93[EUR][1000 genomes]
rs6692062	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs6693927	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs6698361	0.97[EUR][1000 genomes]
rs6704105	0.91[CHB][hapmap]
rs678960	0.97[ASN][1000 genomes]
rs679378	0.97[ASN][1000 genomes]
rs682472	0.82[ASN][1000 genomes]
rs682473	0.83[ASN][1000 genomes]
rs684305	0.97[ASN][1000 genomes]
rs7417180	0.84[ASN][1000 genomes]
rs7521181	0.84[ASN][1000 genomes]
rs7531076	0.94[EUR][1000 genomes]
rs7532166	0.93[EUR][1000 genomes]
rs7540609	0.98[EUR][1000 genomes]
rs7543689	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs7546648	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs7548977	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7551791	0.98[EUR][1000 genomes]
rs7556517	0.82[CHB][hapmap]
rs821755	0.95[CHB][hapmap]
rs946095	0.97[ASN][1000 genomes]
rs946096	0.97[ASN][1000 genomes]
rs946098	0.91[CHB][hapmap]
rs946099	0.91[CHB][hapmap]
rs946100	0.91[CHB][hapmap]
rs946101	0.91[CHB][hapmap]
rs9659389	0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs9659623	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv1003756	chr1:152944201-153044621	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	esv3416199	chr1:152957887-153005113	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4845513	SPRR1B	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152994200-153000000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:152997200-152999800	Enhancers	NHEK	skin
3	chr1:152997400-152998600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:152997800-152999000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:152998000-152999200	Enhancers	HMEC	breast

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