Variant report

Variant	rs721022
Chromosome Location	chr3:160223032-160223033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160220685..160224773-chr3:160234023..160237053,3	MCF-7	breast:
2	chr3:160221864..160223670-chr3:160224243..160226921,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10212236	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10513551	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs1317365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13403	0.80[CEU][hapmap];0.82[GIH][hapmap]
rs1451761	0.80[CEU][hapmap];0.80[GIH][hapmap]
rs1451762	0.80[CEU][hapmap]
rs1451763	0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1551190	0.83[GIH][hapmap]
rs17236544	0.84[CEU][hapmap]
rs17570467	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs1882126	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs1882127	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs1920642	0.84[CEU][hapmap]
rs1920664	0.82[ASW][hapmap];0.84[CEU][hapmap]
rs1953506	0.84[CEU][hapmap]
rs2152425	0.88[ASW][hapmap];0.81[GIH][hapmap]
rs2279457	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs2305407	0.87[CEU][hapmap]
rs28705750	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2886825	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35730266	0.88[ASN][1000 genomes]
rs3773372	0.84[CEU][hapmap];0.85[GIH][hapmap];0.81[EUR][1000 genomes]
rs3851364	0.85[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap]
rs3851366	0.80[CEU][hapmap]
rs41272947	0.82[AMR][1000 genomes]
rs4679881	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs4679885	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs4679888	0.80[EUR][1000 genomes]
rs4679889	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4679890	0.92[CEU][hapmap];0.84[GIH][hapmap]
rs4679891	0.84[CEU][hapmap]
rs4679897	0.80[EUR][1000 genomes]
rs4679899	0.84[CEU][hapmap]
rs4680579	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs4680580	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs4680585	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs4680588	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs58322641	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6441313	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs6441314	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs6441319	0.82[ASW][hapmap];0.83[CEU][hapmap];0.81[GIH][hapmap];0.85[LWK][hapmap];0.82[AMR][1000 genomes]
rs6441320	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs6441324	0.84[CEU][hapmap]
rs6768975	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs6789211	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6798668	0.88[CEU][hapmap]
rs6801300	0.80[CEU][hapmap]
rs6803828	0.80[CEU][hapmap]
rs6809313	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs721023	0.82[ASW][hapmap];0.88[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7356111	0.80[AMR][1000 genomes]
rs7611130	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs7618974	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs7621724	0.88[CEU][hapmap]
rs7627749	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7627756	0.82[ASW][hapmap];0.92[CEU][hapmap];0.85[GIH][hapmap];0.85[LWK][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7629	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs7629423	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7631792	0.80[CEU][hapmap];0.80[GIH][hapmap]
rs7632307	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7634108	0.83[CEU][hapmap]
rs7634826	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs7640072	0.84[CEU][hapmap]
rs7643779	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs7645832	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7647873	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs869468	0.80[CEU][hapmap];0.80[GIH][hapmap]
rs9862595	0.82[ASW][hapmap];0.88[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs9968151	0.80[CEU][hapmap];0.81[GIH][hapmap]

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	esv1797113	chr3:160217483-160245980	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs721022	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160204000-160224000	Weak transcription	Gastric	stomach
2	chr3:160204000-160238200	Weak transcription	Small Intestine	intestine
3	chr3:160204200-160224400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:160204200-160224800	Weak transcription	GM12878-XiMat	blood
5	chr3:160204200-160225400	Weak transcription	Fetal Kidney	kidney
6	chr3:160213000-160228600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:160213600-160223800	Weak transcription	Psoas Muscle	Psoas
8	chr3:160215000-160225400	Weak transcription	Fetal Heart	heart
9	chr3:160215600-160228200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:160215600-160254200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:160215800-160223400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:160215800-160227400	Strong transcription	Primary B cells from cord blood	blood
13	chr3:160215800-160227800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:160215800-160227800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:160215800-160227800	Strong transcription	NHDF-Ad	bronchial
16	chr3:160215800-160228200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:160215800-160254000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:160215800-160254200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:160215800-160254200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:160216000-160227800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:160216000-160227800	Strong transcription	Placenta	Placenta
22	chr3:160216000-160228000	Strong transcription	Duodenum Mucosa	Duodenum
23	chr3:160216000-160254200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr3:160216200-160227800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:160216200-160227800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:160216200-160227800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:160216200-160227800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:160216200-160227800	Strong transcription	Adipose Nuclei	Adipose
29	chr3:160216200-160228600	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:160216200-160249200	Strong transcription	Liver	Liver
31	chr3:160216200-160254200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:160216400-160228200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr3:160216400-160228800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:160216400-160254400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:160216800-160224600	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr3:160216800-160225400	Strong transcription	Hela-S3	cervix
37	chr3:160216800-160253800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:160217000-160226600	Weak transcription	Brain Angular Gyrus	brain
39	chr3:160217000-160227800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:160217200-160225400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:160217200-160254000	Strong transcription	Dnd41	blood
42	chr3:160217400-160225400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:160217400-160227800	Strong transcription	HSMM	muscle
44	chr3:160217400-160228000	Strong transcription	Osteobl	bone
45	chr3:160217400-160259600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr3:160217600-160227800	Strong transcription	NH-A	brain
47	chr3:160217800-160235000	Weak transcription	Fetal Brain Male	brain
48	chr3:160218200-160227800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:160218200-160228400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:160218400-160227800	Strong transcription	Primary B cells from peripheral blood	blood

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