Variant report

Variant	rs2123003
Chromosome Location	chr3:160261744-160261745
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160243184..160245065-chr3:160260331..160263083,2	K562	blood:
2	chr3:160260727..160262696-chr3:160282137..160283785,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229320	Chromatin interaction
ENSG00000186432	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11721112	0.83[AFR][1000 genomes]
rs12152435	0.81[AFR][1000 genomes]
rs12638633	0.81[AFR][1000 genomes]
rs12639488	0.84[AFR][1000 genomes]
rs1369666	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1971128	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3732706	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3851365	0.85[ASN][1000 genomes]
rs4679654	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4679892	0.83[AFR][1000 genomes]
rs4679895	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4679896	0.81[ASN][1000 genomes]
rs4680589	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680591	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56156703	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73875290	0.81[AFR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2123003	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160219800-160263600	Weak transcription	Right Ventricle	heart
2	chr3:160234600-160281000	Weak transcription	Aorta	Aorta
3	chr3:160235000-160266600	Weak transcription	Esophagus	oesophagus
4	chr3:160239600-160265200	Weak transcription	Brain Substantia Nigra	brain
5	chr3:160240200-160280400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:160244200-160272200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:160244400-160263400	Weak transcription	Small Intestine	intestine
8	chr3:160245200-160262200	Weak transcription	Fetal Kidney	kidney
9	chr3:160246600-160279200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:160246800-160266400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:160247000-160270400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:160247000-160281000	Weak transcription	Thymus	Thymus
13	chr3:160248800-160263000	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:160248800-160268600	Weak transcription	NHLF	lung
15	chr3:160249200-160279000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:160250400-160271600	Weak transcription	HepG2	liver
17	chr3:160251000-160266800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:160251200-160282000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:160251600-160263400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:160251800-160263000	Weak transcription	GM12878-XiMat	blood
21	chr3:160252400-160267200	Weak transcription	Primary B cells from cord blood	blood
22	chr3:160252800-160272600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:160253000-160263400	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:160253000-160264800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:160253000-160267400	Weak transcription	Fetal Intestine Small	intestine
26	chr3:160253000-160272000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:160253200-160265200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:160253400-160262200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:160253400-160265200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:160253400-160266200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr3:160253400-160268000	Weak transcription	Liver	Liver
32	chr3:160253600-160263400	Weak transcription	Fetal Lung	lung
33	chr3:160253600-160265600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:160253600-160267800	Weak transcription	NHEK	skin
35	chr3:160254000-160265200	Weak transcription	HUVEC	blood vessel
36	chr3:160254000-160272600	Weak transcription	Hela-S3	cervix
37	chr3:160254000-160279800	Weak transcription	Placenta	Placenta
38	chr3:160254200-160267400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr3:160254200-160268000	Weak transcription	Fetal Intestine Large	intestine
40	chr3:160254200-160278800	Weak transcription	HMEC	breast
41	chr3:160255200-160262200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:160255600-160262800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:160256600-160267400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:160256800-160265800	Weak transcription	Primary T cells from cord blood	blood
45	chr3:160257000-160263200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:160257600-160266200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:160258600-160262800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:160258600-160273800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:160258800-160279000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:160259000-160263000	Weak transcription	HSMM	muscle

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