Variant report

Variant	rs6441370
Chromosome Location	chr3:160993754-160993755
allele	C/T
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	chr3:160980523..160999163-chr3:161073509..161094838,104	MCF-7	breast:
2	chr3:160992262..160994314-chr3:161049627..161053017,3	MCF-7	breast:
3	chr3:160992723..160996276-chr3:161021665..161023883,3	MCF-7	breast:
4	chr3:160992583..160995712-chr3:161006155..161008165,3	MCF-7	breast:
5	chr3:160988830..160994238-chr3:161038778..161044420,11	MCF-7	breast:
6	chr3:160977108..160997706-chr3:161077424..161093939,169	MCF-7	breast:
7	chr3:160991306..160994185-chr3:161000155..161002756,4	MCF-7	breast:
8	chr3:160987260..160989063-chr3:160992148..160994885,3	MCF-7	breast:
9	chr3:160936882..160947576-chr3:160982516..160994324,28	MCF-7	breast:
10	chr3:160991910..160993878-chr3:161070380..161072426,2	MCF-7	breast:
11	chr3:160984342..160995741-chr3:161044454..161065477,51	MCF-7	breast:
12	chr3:160991443..160993916-chr3:161034592..161038621,3	MCF-7	breast:
13	chr3:160990337..160994329-chr3:161056046..161062548,7	MCF-7	breast:
14	chr3:160979328..160995719-chr3:161119748..161144811,174	MCF-7	breast:
15	chr3:160982688..160996909-chr3:161122010..161144833,109	MCF-7	breast:
16	chr3:160990275..160995115-chr3:161003197..161013240,19	MCF-7	breast:
17	chr3:160992668..160995441-chr3:161067329..161069400,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000240567	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000243838	Chromatin interaction
ENSG00000240138	Chromatin interaction
ENSG00000169251	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];0.86[EUR][1000 genomes]
rs1154701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12486253	0.89[EUR][1000 genomes]
rs12493960	0.83[AMR][1000 genomes]
rs12495310	0.89[EUR][1000 genomes]
rs13083229	0.89[EUR][1000 genomes]
rs1382427	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1382428	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1478565	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1478568	0.90[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];0.86[EUR][1000 genomes]
rs1609688	0.83[AMR][1000 genomes]
rs163328	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs189270	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1993891	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2404340	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28515190	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs336541	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs336543	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs336548	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs336567	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336568	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs336569	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336570	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336577	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs336579	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336580	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs336582	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs336583	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336585	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336586	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336589	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336590	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336591	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs336593	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs339101	0.87[AMR][1000 genomes]
rs3849524	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4273380	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4290817	0.87[EUR][1000 genomes]
rs4350933	0.88[EUR][1000 genomes]
rs4370045	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4414866	0.86[AMR][1000 genomes]
rs4470535	0.89[EUR][1000 genomes]
rs4493448	0.87[EUR][1000 genomes]
rs4518145	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4560315	0.89[EUR][1000 genomes]
rs456611	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs457272	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs459515	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs459697	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4597724	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs460165	0.81[AMR][1000 genomes]
rs460508	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs462514	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs463928	0.82[AMR][1000 genomes]
rs464766	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4856714	0.88[EUR][1000 genomes]
rs4856738	0.89[EUR][1000 genomes]
rs4856739	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4856767	0.90[EUR][1000 genomes]
rs4856768	0.90[EUR][1000 genomes]
rs55688744	0.85[EUR][1000 genomes]
rs62279921	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6441371	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];0.87[EUR][1000 genomes]
rs6762645	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6765269	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6765270	0.83[AMR][1000 genomes]
rs6768818	0.87[EUR][1000 genomes]
rs6774276	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6775627	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6789388	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6791213	0.86[EUR][1000 genomes]
rs6794601	0.86[EUR][1000 genomes]
rs6809256	0.87[EUR][1000 genomes]
rs7611367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613227	0.85[EUR][1000 genomes]
rs7613358	0.87[EUR][1000 genomes]
rs7615592	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7623206	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7627528	0.90[EUR][1000 genomes]
rs7629987	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7632797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633186	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636941	0.88[EUR][1000 genomes]
rs7638668	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7647327	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7652267	0.88[EUR][1000 genomes]
rs7653233	0.90[EUR][1000 genomes]
rs7653361	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs899275	0.86[EUR][1000 genomes]
rs9290073	0.85[EUR][1000 genomes]
rs9290074	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs975323	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9790314	0.90[EUR][1000 genomes]
rs9809522	0.89[EUR][1000 genomes]
rs9815222	0.90[EUR][1000 genomes]
rs9821201	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9834659	0.89[EUR][1000 genomes]
rs9839527	0.90[EUR][1000 genomes]
rs9846756	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9850455	0.90[EUR][1000 genomes]
rs9870059	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9872514	0.86[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
rs6441370	SPTSSB	cis	Heart Left Ventricle	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:160970400-160995600	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:160970800-160995600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:160971000-160993800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:160971000-160995400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:160971000-160995400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:160971200-160995200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:160971200-160996000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:160972200-160996600	Weak transcription	Brain Substantia Nigra	brain
10	chr3:160972400-160993800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:160972800-160995400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:160975400-160995800	Weak transcription	Fetal Intestine Large	intestine
13	chr3:160976600-160995400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:160979200-160999800	Weak transcription	Psoas Muscle	Psoas
15	chr3:160982200-160994000	Weak transcription	Fetal Brain Female	brain
16	chr3:160982200-160994200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:160982200-160994400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:160982200-160994600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:160982200-160995000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:160982200-160995400	Weak transcription	Aorta	Aorta
21	chr3:160982400-160996600	Weak transcription	Adipose Nuclei	Adipose
22	chr3:160984400-160994000	Weak transcription	Fetal Intestine Small	intestine
23	chr3:160984800-160995200	Weak transcription	A549	lung
24	chr3:160984800-161002400	Weak transcription	NHEK	skin
25	chr3:160985200-160996600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:160988000-160996200	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:160989000-161000400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:160991800-160994400	Enhancers	Stomach Mucosa	stomach
29	chr3:160991800-160996000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:160992200-160995200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:160992400-160994000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:160992400-160994400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:160992600-160994400	Strong transcription	Left Ventricle	heart
34	chr3:160993000-160993800	Enhancers	HepG2	liver
35	chr3:160993000-160994400	Strong transcription	Liver	Liver
36	chr3:160993000-160994400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:160993000-160994600	Enhancers	Esophagus	oesophagus
38	chr3:160993200-160994000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:160993200-160994200	Strong transcription	Gastric	stomach
40	chr3:160993200-160994400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:160993200-160994600	Strong transcription	Right Ventricle	heart
42	chr3:160993200-160994800	Strong transcription	HSMM	muscle
43	chr3:160993400-160994000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:160993400-160994200	Strong transcription	Fetal Muscle Leg	muscle
45	chr3:160993400-160994400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:160993400-160994400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:160993400-160994400	Strong transcription	Pancreas	Pancrea
48	chr3:160993400-160994400	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr3:160993600-160994000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:160993600-160994000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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