Variant report

Variant	rs7629202
Chromosome Location	chr3:160169197-160169198
allele	C/T
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	MEF2A	chr3:160168483-160169326	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr3:160168492-160169214	SK-N-SH	brain:	n/a	chr3:160168986-160168995
3	RCOR1	chr3:160166746-160169584	IMR90	lung:	n/a	n/a
4	TCF12	chr3:160168436-160169223	SK-N-SH	brain:	n/a	chr3:160168986-160168995
5	TEAD4	chr3:160168441-160169216	SK-N-SH	brain:	n/a	n/a
6	ZNF384	chr3:160169188-160169563	K562	blood:	n/a	n/a
7	GATA3	chr3:160168455-160169209	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:160116116..160127665-chr3:160158037..160169627,42	K562	blood:
2	chr3:160167035..160169821-chr3:160232708..160234646,2	K562	blood:
3	chr3:160113853..160115916-chr3:160167790..160169810,2	K562	blood:
4	chr3:160166836..160169216-chr3:161090028..161092220,2	MCF-7	breast:
5	chr3:160167702..160169385-chr3:160272825..160274892,2	K562	blood:
6	chr3:160164471..160170330-chr3:160281681..160284179,8	K562	blood:

Variant related genes	Relation type
TRIM59	TF binding region
ENSG00000248710	TF binding region
ENSG00000244009	TF binding region
ENSG00000196542	Chromatin interaction
ENSG00000207779	Chromatin interaction
ENSG00000068885	Chromatin interaction
ENSG00000113810	Chromatin interaction
ENSG00000238741	Chromatin interaction
ENSG00000198987	Chromatin interaction
ENSG00000229320	Chromatin interaction
ENSG00000186432	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10212236	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10513551	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11918749	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13403	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1451761	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1451762	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1451764	0.85[EUR][1000 genomes]
rs1551190	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1584688	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17236544	0.84[ASN][1000 genomes]
rs1882127	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1920642	0.84[ASN][1000 genomes]
rs1920662	0.84[ASN][1000 genomes]
rs1920664	0.84[ASN][1000 genomes]
rs1953506	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2152425	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2279457	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305407	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28705750	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2886825	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3773372	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3851366	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4091703	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41272947	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4621370	0.84[ASN][1000 genomes]
rs4679881	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4679885	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4679888	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4679889	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4679890	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4679891	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4679899	0.84[ASN][1000 genomes]
rs4680576	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680579	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4680580	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4680585	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680587	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680588	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55687857	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55731730	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56197102	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56394279	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58322641	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58665246	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60009222	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60460891	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62272186	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62272791	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62272792	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62272794	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62272800	0.85[EUR][1000 genomes]
rs6441313	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441314	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6441319	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6441320	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441324	0.84[ASN][1000 genomes]
rs6768975	0.84[ASN][1000 genomes]
rs6791261	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6792612	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6793560	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6798668	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6801300	0.84[ASN][1000 genomes]
rs6803828	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6808083	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs721023	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73154592	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7356111	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7611130	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7618974	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7621724	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7624902	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7627749	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7627756	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7629	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7631792	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7634108	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7634826	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7640072	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7643779	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7645832	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7647873	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs869468	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9798898	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9799314	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9862595	0.84[ASN][1000 genomes]
rs9968151	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[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	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	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7629202	SMC4	Cis_1M	lymphoblastoid	RTeQTL
rs7629202	SMC4,MIR15B,MIR16-2	cis	brain	BrainEAC

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160168000-160169800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:160168400-160169400	Weak transcription	Hela-S3	cervix
3	chr3:160168400-160169600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:160168400-160169600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:160168400-160170200	Weak transcription	Lung	lung
6	chr3:160168400-160172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:160168400-160172600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:160168400-160172800	Weak transcription	Brain Anterior Caudate	brain
9	chr3:160168600-160169600	Flanking Active TSS	K562	blood
10	chr3:160168600-160169600	Enhancers	NHLF	lung
11	chr3:160168600-160169800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:160168600-160169800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:160168600-160169800	Enhancers	HSMM	muscle
14	chr3:160168600-160169800	Enhancers	HUVEC	blood vessel
15	chr3:160168600-160169800	Enhancers	NHDF-Ad	bronchial
16	chr3:160168600-160170200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:160168800-160169200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:160168800-160169200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:160168800-160169600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:160168800-160169600	Enhancers	HSMMtube	muscle
21	chr3:160168800-160169600	Enhancers	NH-A	brain
22	chr3:160168800-160169600	Enhancers	Osteobl	bone
23	chr3:160168800-160169800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:160168800-160169800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:160168800-160169800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr3:160169000-160169400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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