Variant report

Variant	rs1451764
Chromosome Location	chr3:160270121-160270122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160216490..160219028-chr3:160268486..160271353,2	K562	blood:
2	chr3:160268583..160271718-chr3:160281791..160284815,6	MCF-7	breast:
3	chr3:160180220..160182698-chr3:160269004..160270777,2	K562	blood:
4	chr3:160270076..160273601-chr3:160274357..160279300,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229320	Chromatin interaction
ENSG00000186432	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10212236	0.89[EUR][1000 genomes]
rs13403	0.82[EUR][1000 genomes]
rs1551190	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1584688	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17236544	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17570467	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1882126	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1882127	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1920642	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1920662	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1920664	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2279457	0.83[EUR][1000 genomes]
rs2366969	0.86[EUR][1000 genomes]
rs28705750	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2886825	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732707	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773372	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3851366	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4091703	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4292273	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4292274	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4621370	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679654	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4679655	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4679885	0.82[EUR][1000 genomes]
rs4679888	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4679889	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4679890	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679891	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679896	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4679899	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679900	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680585	0.83[EUR][1000 genomes]
rs4680587	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4680588	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4680591	0.84[AMR][1000 genomes]
rs56197102	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56394279	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58322641	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60460891	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62272791	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62272792	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62272794	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272800	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272810	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441320	0.81[EUR][1000 genomes]
rs6441324	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6768975	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6798668	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6801300	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6806505	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6808083	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs721023	0.89[EUR][1000 genomes]
rs7618974	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7621724	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7627749	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7627756	0.88[EUR][1000 genomes]
rs7629	0.82[EUR][1000 genomes]
rs7629202	0.85[EUR][1000 genomes]
rs7631792	0.82[EUR][1000 genomes]
rs7634826	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7640072	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643779	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7644453	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645832	0.89[EUR][1000 genomes]
rs7647873	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9862595	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription 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 miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	nsv877701	chr3:160228001-160283815	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
8	nsv877702	chr3:160262803-160304614	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1451764	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160234600-160281000	Weak transcription	Aorta	Aorta
2	chr3:160240200-160280400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:160244200-160272200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:160246600-160279200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:160247000-160270400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:160247000-160281000	Weak transcription	Thymus	Thymus
7	chr3:160249200-160279000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:160250400-160271600	Weak transcription	HepG2	liver
9	chr3:160251200-160282000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:160252800-160272600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:160253000-160272000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:160254000-160272600	Weak transcription	Hela-S3	cervix
13	chr3:160254000-160279800	Weak transcription	Placenta	Placenta
14	chr3:160254200-160278800	Weak transcription	HMEC	breast
15	chr3:160258600-160273800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:160258800-160279000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:160259200-160277000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:160259800-160272600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:160260200-160271400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:160260200-160279600	Weak transcription	Osteobl	bone
21	chr3:160260600-160271000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:160261000-160271400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:160261800-160281000	Weak transcription	Ovary	ovary
24	chr3:160262000-160272400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:160262600-160277800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:160263600-160270400	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:160263600-160271000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:160263600-160271400	Weak transcription	Adipose Nuclei	Adipose
29	chr3:160264000-160272000	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:160264000-160272600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:160264200-160272200	Weak transcription	Right Atrium	heart
32	chr3:160264200-160282000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:160264400-160270400	Weak transcription	Psoas Muscle	Psoas
34	chr3:160264400-160270400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:160264800-160271000	Weak transcription	Gastric	stomach
36	chr3:160265200-160276800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:160265800-160272400	Weak transcription	Small Intestine	intestine
38	chr3:160266000-160271600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:160266000-160271600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:160266000-160272200	Weak transcription	Right Ventricle	heart
41	chr3:160266000-160272800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:160266200-160271000	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr3:160266400-160271000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:160266400-160271200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:160266400-160277400	Weak transcription	HUVEC	blood vessel
46	chr3:160266800-160272400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr3:160267200-160271000	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr3:160267200-160271400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
49	chr3:160267200-160274600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:160267400-160271200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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