Variant report

Variant	rs4679886
Chromosome Location	chr3:160155047-160155048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160150419..160152165-chr3:160152577..160155535,2	MCF-7	breast:
2	chr3:160146751..160150708-chr3:160150793..160158045,9	K562	blood:
3	chr3:160154300..160157981-chr3:160166786..160169442,5	MCF-7	breast:
4	chr3:160152431..160159028-chr3:160159168..160164097,7	MCF-7	breast:
5	chr3:160127401..160129476-chr3:160154855..160157370,2	K562	blood:

Variant related genes	Relation type
ENSG00000213186	Chromatin interaction
ENSG00000113810	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936201	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10936203	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11708118	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11709232	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11709336	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11716413	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11719750	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720689	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11721112	0.80[EUR][1000 genomes]
rs12152435	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12630564	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12630770	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12630956	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12638633	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12639488	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16831207	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17236494	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17826137	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17826173	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17826257	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1873076	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1920663	0.81[EUR][1000 genomes]
rs2095529	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2099496	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2275151	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3773369	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4679892	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4680581	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680586	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56952700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60395700	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6441311	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73875254	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73875259	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73875285	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73875290	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7644186	0.80[EUR][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	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
8	nsv822306	chr3:160153049-160157348	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4679886	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160120200-160164400	Weak transcription	Fetal Brain Male	brain
2	chr3:160121200-160157200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:160121200-160157400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:160121200-160157800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:160122000-160161000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:160122000-160164400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:160122000-160164600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:160122200-160157400	Strong transcription	Fetal Thymus	thymus
9	chr3:160122600-160156600	Strong transcription	K562	blood
10	chr3:160123200-160155400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:160124000-160159000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:160125200-160159800	Strong transcription	HSMM	muscle
13	chr3:160127800-160157000	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr3:160128400-160157200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:160128600-160158200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:160129600-160156600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:160129600-160157000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:160130000-160166200	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:160130400-160157400	Strong transcription	NH-A	brain
20	chr3:160132000-160158800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr3:160132200-160157000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:160133800-160164600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:160134600-160156800	Strong transcription	HUVEC	blood vessel
24	chr3:160134800-160158800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:160135000-160159200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:160136800-160157400	Strong transcription	NHDF-Ad	bronchial
27	chr3:160137800-160158800	Strong transcription	Primary B cells from cord blood	blood
28	chr3:160139600-160157000	Strong transcription	Fetal Lung	lung
29	chr3:160140800-160166600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:160142400-160164400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:160143400-160156400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr3:160143600-160156600	Strong transcription	Primary hematopoietic stem cells	blood
33	chr3:160143600-160166600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:160143800-160156800	Strong transcription	Fetal Intestine Large	intestine
35	chr3:160145000-160156200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:160145600-160166800	Weak transcription	Right Atrium	heart
37	chr3:160145800-160157000	Weak transcription	Psoas Muscle	Psoas
38	chr3:160146000-160160000	Weak transcription	Ovary	ovary
39	chr3:160146000-160162400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:160146000-160164400	Weak transcription	Gastric	stomach
41	chr3:160146000-160165400	Weak transcription	Aorta	Aorta
42	chr3:160146000-160167000	Weak transcription	Pancreas	Pancrea
43	chr3:160146400-160166200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:160146800-160160000	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:160147000-160164400	Weak transcription	Esophagus	oesophagus
46	chr3:160147000-160166200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr3:160147400-160155600	Weak transcription	Colonic Mucosa	Colon
48	chr3:160147800-160164400	Weak transcription	Lung	lung
49	chr3:160150000-160157200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:160150000-160160600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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