Variant report

Variant	rs4679892
Chromosome Location	chr3:160264266-160264267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160263639..160265252-chr3:160357091..160359879,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10923	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10936201	0.83[EUR][1000 genomes]
rs10936203	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11708118	0.83[EUR][1000 genomes]
rs11709232	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11711627	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11712392	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11713230	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11716413	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11719750	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11720689	0.82[EUR][1000 genomes]
rs11721112	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12152435	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12630564	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12630770	0.81[EUR][1000 genomes]
rs12630956	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12638633	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12639488	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13065269	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13074231	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16831207	0.83[EUR][1000 genomes]
rs17236494	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17826137	0.82[EUR][1000 genomes]
rs17826173	0.83[EUR][1000 genomes]
rs17826257	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1873076	0.82[EUR][1000 genomes]
rs1920663	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2095529	0.82[EUR][1000 genomes]
rs2099496	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2123003	0.83[AFR][1000 genomes]
rs2141668	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2178451	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35008770	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3773369	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4679886	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4679903	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4679904	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4680581	0.83[EUR][1000 genomes]
rs4680586	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56952700	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60395700	0.83[EUR][1000 genomes]
rs6441311	0.82[EUR][1000 genomes]
rs73875259	0.84[EUR][1000 genomes]
rs73875285	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73875290	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7644186	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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
rs4679892	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160234600-160281000	Weak transcription	Aorta	Aorta
2	chr3:160235000-160266600	Weak transcription	Esophagus	oesophagus
3	chr3:160239600-160265200	Weak transcription	Brain Substantia Nigra	brain
4	chr3:160240200-160280400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:160244200-160272200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:160246600-160279200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:160246800-160266400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:160247000-160270400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:160247000-160281000	Weak transcription	Thymus	Thymus
10	chr3:160248800-160268600	Weak transcription	NHLF	lung
11	chr3:160249200-160279000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:160250400-160271600	Weak transcription	HepG2	liver
13	chr3:160251000-160266800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:160251200-160282000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:160252400-160267200	Weak transcription	Primary B cells from cord blood	blood
16	chr3:160252800-160272600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:160253000-160264800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:160253000-160267400	Weak transcription	Fetal Intestine Small	intestine
19	chr3:160253000-160272000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:160253200-160265200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:160253400-160265200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:160253400-160266200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:160253400-160268000	Weak transcription	Liver	Liver
24	chr3:160253600-160265600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:160253600-160267800	Weak transcription	NHEK	skin
26	chr3:160254000-160265200	Weak transcription	HUVEC	blood vessel
27	chr3:160254000-160272600	Weak transcription	Hela-S3	cervix
28	chr3:160254000-160279800	Weak transcription	Placenta	Placenta
29	chr3:160254200-160267400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr3:160254200-160268000	Weak transcription	Fetal Intestine Large	intestine
31	chr3:160254200-160278800	Weak transcription	HMEC	breast
32	chr3:160256600-160267400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:160256800-160265800	Weak transcription	Primary T cells from cord blood	blood
34	chr3:160257600-160266200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:160258600-160273800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:160258800-160279000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:160259000-160265200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:160259000-160269200	Weak transcription	NH-A	brain
39	chr3:160259200-160277000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:160259800-160272600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:160260200-160268200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:160260200-160271400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:160260200-160279600	Weak transcription	Osteobl	bone
44	chr3:160260400-160265200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:160260400-160265400	Weak transcription	Stomach Mucosa	stomach
46	chr3:160260400-160266800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:160260400-160268400	Weak transcription	NHDF-Ad	bronchial
48	chr3:160260600-160266000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr3:160260600-160268000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:160260600-160271000	Weak transcription	Rectal Smooth Muscle	rectum

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