Variant report

Variant	rs6441371
Chromosome Location	chr3:161008727-161008728
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:161000404..161005732-chr3:161006848..161011862,5	MCF-7	breast:
2	chr3:160818828..160822903-chr3:161006753..161012586,7	MCF-7	breast:
3	chr3:161006807..161008935-chr3:161043200..161045858,2	MCF-7	breast:
4	chr3:161006306..161018540-chr3:161080036..161092321,36	MCF-7	breast:
5	chr3:161006869..161011120-chr3:161039575..161043501,7	MCF-7	breast:
6	chr3:161006300..161011924-chr3:161012842..161019057,8	MCF-7	breast:
7	chr3:160990275..160995115-chr3:161003197..161013240,19	MCF-7	breast:
8	chr3:160985097..160988877-chr3:161008569..161012184,4	MCF-7	breast:
9	chr3:161003253..161016100-chr3:161121496..161137189,33	MCF-7	breast:
10	chr3:161006588..161008240-chr3:161008260..161009929,2	MCF-7	breast:
11	chr3:161006401..161012112-chr3:161031973..161037314,13	MCF-7	breast:
12	chr20:49347409..49350035-chr3:161007609..161009376,2	MCF-7	breast:
13	chr3:161004827..161016513-chr3:161081728..161095319,56	MCF-7	breast:
14	chr3:161001819..161012846-chr3:161052557..161065154,32	MCF-7	breast:
15	chr3:160995830..160998585-chr3:161007446..161010411,2	MCF-7	breast:
16	chr3:161007104..161011008-chr3:161031241..161034660,5	MCF-7	breast:
17	chr3:161007555..161015806-chr3:161127103..161142651,19	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000124171	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000240138	Chromatin interaction
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10804790	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1154701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12486253	0.87[EUR][1000 genomes]
rs12493960	0.83[AMR][1000 genomes]
rs12495310	0.87[EUR][1000 genomes]
rs13083229	0.87[EUR][1000 genomes]
rs1382427	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1382428	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1478565	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1478568	0.88[EUR][1000 genomes]
rs1599374	0.83[AMR][1000 genomes]
rs1599376	0.83[AMR][1000 genomes]
rs1599378	0.83[AMR][1000 genomes]
rs1600209	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1609688	0.83[AMR][1000 genomes]
rs163328	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs189270	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1993891	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2404340	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28515190	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs336541	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs336543	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs336548	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs336567	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs336568	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs336569	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs336570	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs336577	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336579	0.84[AMR][1000 genomes]
rs336580	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs336582	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs336583	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs336585	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs336586	0.90[AMR][1000 genomes]
rs336589	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs336590	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs336591	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs336593	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs339101	0.87[AMR][1000 genomes]
rs3849524	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4273380	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4290817	0.85[EUR][1000 genomes]
rs4350933	0.86[EUR][1000 genomes]
rs4370045	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4414866	0.86[AMR][1000 genomes]
rs4470535	0.87[EUR][1000 genomes]
rs4493448	0.85[EUR][1000 genomes]
rs4518145	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4560315	0.87[EUR][1000 genomes]
rs456611	0.86[AMR][1000 genomes]
rs457272	0.84[AMR][1000 genomes]
rs459515	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs459697	0.90[AMR][1000 genomes]
rs4597724	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs460165	0.81[AMR][1000 genomes]
rs460508	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs462514	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs463928	0.82[AMR][1000 genomes]
rs464766	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4856714	0.86[EUR][1000 genomes]
rs4856738	0.87[EUR][1000 genomes]
rs4856739	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4856767	0.88[EUR][1000 genomes]
rs4856768	0.88[EUR][1000 genomes]
rs55688744	0.83[EUR][1000 genomes]
rs62279921	0.84[AMR][1000 genomes]
rs6441370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441373	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6762645	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6765269	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6765270	0.83[AMR][1000 genomes]
rs6768818	0.85[EUR][1000 genomes]
rs6774276	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6775627	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6789388	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6791213	0.84[EUR][1000 genomes]
rs6794601	0.84[EUR][1000 genomes]
rs6809256	0.85[EUR][1000 genomes]
rs7611367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7613227	0.83[EUR][1000 genomes]
rs7613358	0.85[EUR][1000 genomes]
rs7615592	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7623206	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7627528	0.88[EUR][1000 genomes]
rs7629987	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7632797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7633186	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7636941	0.86[EUR][1000 genomes]
rs7638668	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7647327	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7652267	0.86[EUR][1000 genomes]
rs7653233	0.88[EUR][1000 genomes]
rs7653361	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs899275	0.84[EUR][1000 genomes]
rs9290073	0.83[EUR][1000 genomes]
rs9290074	0.99[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs975323	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9790314	0.88[EUR][1000 genomes]
rs9809522	0.87[EUR][1000 genomes]
rs9815222	0.88[EUR][1000 genomes]
rs9821201	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9834659	0.87[EUR][1000 genomes]
rs9839527	0.88[EUR][1000 genomes]
rs9846756	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9850455	0.88[EUR][1000 genomes]
rs9870059	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9872514	0.84[EUR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6441371	SPTSSB	cis	Heart Left Ventricle	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160994600-161016800	Weak transcription	Right Ventricle	heart
2	chr3:161003400-161009200	Weak transcription	NHEK	skin
3	chr3:161003600-161009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:161003600-161009000	Weak transcription	HMEC	breast
5	chr3:161008000-161010200	Enhancers	Esophagus	oesophagus
6	chr3:161008200-161010000	Enhancers	Stomach Mucosa	stomach
7	chr3:161008400-161009000	Weak transcription	Gastric	stomach
8	chr3:161008600-161010000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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