Variant report

Variant	rs6810390
Chromosome Location	chr4:16222827-16222828
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:16221619..16226314-chr4:16226369..16230057,8	MCF-7	breast:
2	chr4:16219520..16223580-chr4:16226468..16229712,6	MCF-7	breast:
3	chr4:16210098..16212174-chr4:16220610..16223093,2	K562	blood:
4	chr4:15976147..15979142-chr4:16221984..16223628,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263327	Chromatin interaction
ENSG00000169762	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10017532	0.82[ASN][1000 genomes]
rs10516297	0.94[ASN][1000 genomes]
rs11730922	0.96[ASN][1000 genomes]
rs13110290	0.80[ASN][1000 genomes]
rs13120908	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13132678	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13136055	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13136172	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2028631	0.85[ASN][1000 genomes]
rs28654954	0.84[ASN][1000 genomes]
rs2872216	0.90[ASN][1000 genomes]
rs33980476	0.83[ASN][1000 genomes]
rs34129131	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34496855	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34592687	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34663238	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34837883	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs35141398	0.93[AFR][1000 genomes]
rs35475888	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35517826	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35804424	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35806798	0.99[ASN][1000 genomes]
rs35899968	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35931597	0.85[ASN][1000 genomes]
rs3749544	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4235382	0.86[ASN][1000 genomes]
rs4481232	0.82[ASN][1000 genomes]
rs4571326	0.82[ASN][1000 genomes]
rs4698138	0.81[ASN][1000 genomes]
rs4698457	0.82[ASN][1000 genomes]
rs56353092	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68114846	0.90[AFR][1000 genomes]
rs6823229	0.90[ASN][1000 genomes]
rs6823230	0.90[ASN][1000 genomes]
rs6852432	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995025	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic 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
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv878720	chr4:16222046-16242215	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6810390	TAPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16181200-16223800	Weak transcription	Fetal Brain Male	brain
2	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon
3	chr4:16193200-16225800	Weak transcription	Fetal Brain Female	brain
4	chr4:16198800-16225600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:16198800-16226000	Weak transcription	NHEK	skin
6	chr4:16198800-16226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:16204800-16226600	Weak transcription	NH-A	brain
8	chr4:16205200-16225600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:16207400-16223600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:16208400-16224400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:16208400-16225200	Weak transcription	Fetal Kidney	kidney
12	chr4:16208400-16225800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:16208800-16225600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:16208800-16225600	Weak transcription	Esophagus	oesophagus
15	chr4:16208800-16225600	Weak transcription	Gastric	stomach
16	chr4:16208800-16225800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:16208800-16225800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:16208800-16227200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:16209000-16225600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:16209200-16223400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:16209200-16225600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr4:16209200-16225600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:16209400-16226200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:16209400-16226200	Weak transcription	HSMMtube	muscle
25	chr4:16210400-16225800	Weak transcription	Brain Germinal Matrix	brain
26	chr4:16212200-16226000	Weak transcription	NHDF-Ad	bronchial
27	chr4:16214000-16224400	Weak transcription	Brain Anterior Caudate	brain
28	chr4:16214200-16224200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:16214400-16226800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr4:16214600-16224400	Weak transcription	Brain Angular Gyrus	brain
31	chr4:16214600-16225800	Weak transcription	Placenta	Placenta
32	chr4:16214800-16224200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr4:16214800-16225200	Weak transcription	Hela-S3	cervix
34	chr4:16214800-16225800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:16215000-16223600	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:16215000-16224600	Weak transcription	Colon Smooth Muscle	Colon
37	chr4:16215000-16226000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:16215200-16223400	Weak transcription	Adipose Nuclei	Adipose
39	chr4:16215200-16225000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:16215600-16225600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:16215800-16223800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:16216200-16225600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:16216400-16223600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr4:16216600-16224400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:16216800-16225600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:16218600-16224400	Weak transcription	Small Intestine	intestine
47	chr4:16218600-16224400	Weak transcription	Spleen	Spleen
48	chr4:16218600-16225600	Weak transcription	Lung	lung
49	chr4:16218800-16224200	Weak transcription	Ovary	ovary
50	chr4:16218800-16224400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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