Variant report

Variant	rs4687721
Chromosome Location	chr3:51598254-51598255
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	chr3:51575437..51577336-chr3:51596376..51599200,2	MCF-7	breast:
2	chr3:51593552..51596365-chr3:51596602..51598437,2	K562	blood:

Variant related genes	Relation type
ENSG00000164080	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1055429	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130293	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11719995	0.84[EUR][1000 genomes]
rs11721253	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11917683	1.00[CEU][hapmap]
rs11919197	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap]
rs13090011	0.85[CEU][hapmap]
rs1552074	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs2127655	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs3821829	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4067	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs4234644	1.00[CEU][hapmap]
rs4317086	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4355273	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs4611808	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4687568	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687569	0.84[AMR][1000 genomes]
rs4687734	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6445791	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6771081	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6771491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs6775666	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes]
rs6787312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6793900	0.86[AMR][1000 genomes]
rs6809155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7372658	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9311469	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9866430	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv997264	chr3:51584056-51689648	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536570	chr3:51584056-51689648	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv999553	chr3:51584056-51696052	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4687721	TEX264	cis	Nerve Tibial	GTEx
rs4687721	TEX264	cis	Artery Tibial	GTEx
rs4687721	TEX264	cis	Esophagus Muscularis	GTEx
rs4687721	TEX264	cis	Esophagus Mucosa	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51574000-51600600	Weak transcription	Gastric	stomach
2	chr3:51574000-51615400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:51574000-51624800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:51574200-51616400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:51574400-51613800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:51574600-51600800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:51574600-51601800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:51574600-51624600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:51574800-51624800	Weak transcription	NH-A	brain
10	chr3:51575200-51615600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:51576400-51602000	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:51578600-51607000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:51578800-51600200	Weak transcription	A549	lung
14	chr3:51578800-51624400	Weak transcription	Esophagus	oesophagus
15	chr3:51579000-51602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:51579200-51602400	Weak transcription	HMEC	breast
17	chr3:51580000-51602600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:51584200-51600200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:51584200-51602200	Weak transcription	Pancreas	Pancrea
20	chr3:51584200-51602200	Weak transcription	Spleen	Spleen
21	chr3:51584200-51614200	Weak transcription	Aorta	Aorta
22	chr3:51584800-51600200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:51584800-51602200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:51585000-51615600	Weak transcription	NHEK	skin
25	chr3:51585200-51624400	Weak transcription	Brain Germinal Matrix	brain
26	chr3:51585400-51602000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr3:51585800-51612400	Weak transcription	Fetal Thymus	thymus
28	chr3:51585800-51625000	Weak transcription	Colonic Mucosa	Colon
29	chr3:51586200-51600000	Weak transcription	Stomach Mucosa	stomach
30	chr3:51586400-51601800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:51587800-51607000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:51587800-51624400	Weak transcription	Hela-S3	cervix
33	chr3:51588000-51612600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:51588000-51640000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:51588200-51600600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr3:51588200-51612600	Weak transcription	Lung	lung
37	chr3:51588400-51599000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:51589000-51612400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:51589200-51612400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:51590000-51611800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:51590800-51607000	Weak transcription	GM12878-XiMat	blood
42	chr3:51591000-51606800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:51591200-51601600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr3:51591200-51612600	Weak transcription	Thymus	Thymus
45	chr3:51591400-51602200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:51591400-51612200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:51591600-51602200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:51591600-51607000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:51592200-51607000	Weak transcription	Fetal Intestine Large	intestine
50	chr3:51592800-51607200	Weak transcription	Primary B cells from peripheral blood	blood

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