Variant report

Variant	rs3732707
Chromosome Location	chr3:160286646-160286647
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:160286366-160287084	MCF-7	breast:	n/a	n/a
2	POLR2A	chr3:160286645-160286690	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:160286644-160286752	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:160286339-160286693	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160281906..160285341-chr3:160285654..160289811,8	MCF-7	breast:
2	chr3:160282613..160284767-chr3:160285868..160288833,4	MCF-7	breast:

Variant related genes	Relation type
KPNA4	TF binding region
ENSG00000186432	Chromatin interaction
ENSG00000229320	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10212236	0.83[EUR][1000 genomes]
rs1451764	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1551190	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1584688	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17236544	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17570467	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882126	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882127	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1920642	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1920662	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1920664	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2366969	0.83[EUR][1000 genomes]
rs28705750	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2886825	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3773372	0.90[EUR][1000 genomes]
rs3851366	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4091703	0.80[EUR][1000 genomes]
rs4292273	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4292274	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4621370	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679888	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679889	0.81[EUR][1000 genomes]
rs4679890	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679891	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679895	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4679896	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4679897	0.82[EUR][1000 genomes]
rs4679899	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679900	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680587	0.80[EUR][1000 genomes]
rs56197102	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56394279	0.85[ASN][1000 genomes]
rs58322641	0.82[EUR][1000 genomes]
rs62272791	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62272792	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62272794	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272800	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272810	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441324	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6768975	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6798668	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6801300	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6806505	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808083	0.85[ASN][1000 genomes]
rs721023	0.83[EUR][1000 genomes]
rs7618974	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7621724	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7627749	0.83[EUR][1000 genomes]
rs7627756	0.82[EUR][1000 genomes]
rs7634826	0.86[ASN][1000 genomes]
rs7640072	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7643779	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7644453	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645832	0.83[EUR][1000 genomes]
rs7647873	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9862595	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	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
6	nsv4089	chr3:160284848-160330024	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv963373	chr3:160285741-160287108	ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3732707	SMC4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160284200-160289600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:160284400-160286800	Weak transcription	Fetal Thymus	thymus
3	chr3:160284600-160286800	Weak transcription	Thymus	Thymus
4	chr3:160284600-160287000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:160284600-160288400	Weak transcription	Ovary	ovary
6	chr3:160284800-160287200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:160284800-160287200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:160284800-160287600	Weak transcription	Fetal Intestine Large	intestine
9	chr3:160284800-160287800	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr3:160284800-160288200	Weak transcription	Brain Substantia Nigra	brain
11	chr3:160284800-160288400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:160284800-160289600	Weak transcription	Fetal Lung	lung
13	chr3:160284800-160292000	Weak transcription	Brain Anterior Caudate	brain
14	chr3:160284800-160295000	Weak transcription	Stomach Mucosa	stomach
15	chr3:160284800-160295200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:160285000-160287000	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:160285000-160287200	Weak transcription	GM12878-XiMat	blood
18	chr3:160285000-160287400	Enhancers	Dnd41	blood
19	chr3:160285000-160287800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:160285000-160287800	Weak transcription	Liver	Liver
21	chr3:160285000-160289600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:160285000-160290800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:160285000-160292200	Weak transcription	Primary B cells from cord blood	blood
24	chr3:160285200-160287000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:160285200-160287600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:160285200-160287600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:160285200-160287800	Weak transcription	Psoas Muscle	Psoas
28	chr3:160285200-160288000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:160285200-160289600	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:160285200-160293400	Weak transcription	HepG2	liver
31	chr3:160285200-160294400	Weak transcription	HSMMtube	muscle
32	chr3:160285200-160298800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:160285400-160286800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:160285400-160286800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr3:160285400-160288000	Weak transcription	NHDF-Ad	bronchial
36	chr3:160285400-160288400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:160285600-160286800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:160285600-160286800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
39	chr3:160285600-160286800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:160285600-160286800	Strong transcription	NHLF	lung
41	chr3:160285600-160287000	Strong transcription	Placenta	Placenta
42	chr3:160285600-160287200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:160285600-160287200	Strong transcription	Fetal Intestine Small	intestine
44	chr3:160285600-160287200	ZNF genes & repeats	Fetal Stomach	stomach
45	chr3:160285600-160287400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:160285600-160287400	Weak transcription	Hela-S3	cervix
47	chr3:160285600-160287400	Weak transcription	HUVEC	blood vessel
48	chr3:160285600-160289200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr3:160285800-160286800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:160285800-160286800	Strong transcription	Primary hematopoietic stem cells	blood

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