Variant report

Variant	rs59295369
Chromosome Location	chr16:69774860-69774861
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69765023..69767950-chr16:69774599..69776546,3	MCF-7	breast:
2	chr16:69768952..69770830-chr16:69774637..69776379,2	MCF-7	breast:
3	chr16:69760111..69762004-chr16:69774440..69775982,2	K562	blood:
4	chr16:69774416..69776982-chr8:145016470..145018843,2	MCF-7	breast:
5	chr16:69755773..69764501-chr16:69767489..69780977,30	MCF-7	breast:
6	chr16:69759462..69761611-chr16:69773945..69776080,3	K562	blood:

Variant related genes	Relation type
ENSG00000262136	Chromatin interaction
ENSG00000178209	Chromatin interaction
ENSG00000181019	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10048108	0.84[AFR][1000 genomes]
rs10163235	0.84[AFR][1000 genomes]
rs11075733	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11075734	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1139178	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11641521	0.82[EUR][1000 genomes]
rs11643926	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11644838	0.82[EUR][1000 genomes]
rs11644914	0.81[EUR][1000 genomes]
rs12596679	0.82[EUR][1000 genomes]
rs12925371	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1437135	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1865965	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2196574	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2361839	0.81[AMR][1000 genomes]
rs3811349	0.86[ASN][1000 genomes]
rs4078387	0.82[EUR][1000 genomes]
rs4464069	0.82[EUR][1000 genomes]
rs4580150	0.82[EUR][1000 genomes]
rs4985518	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985523	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55701476	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55863174	0.81[EUR][1000 genomes]
rs55992518	0.82[EUR][1000 genomes]
rs56282083	0.81[EUR][1000 genomes]
rs57518557	0.81[EUR][1000 genomes]
rs57565297	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60231938	0.81[EUR][1000 genomes]
rs61426398	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6499253	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs689455	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7186002	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7189424	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73579458	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8045682	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8059345	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv524364	chr16:69745145-69803443	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59295369	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69761200-69775400	Weak transcription	Fetal Brain Male	brain
2	chr16:69761200-69776200	Weak transcription	Ovary	ovary
3	chr16:69761800-69787400	Weak transcription	Right Atrium	heart
4	chr16:69762200-69776400	Weak transcription	Small Intestine	intestine
5	chr16:69762400-69775200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr16:69762800-69775000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr16:69766000-69776400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr16:69766600-69775400	Weak transcription	Stomach Mucosa	stomach
9	chr16:69767800-69775200	Weak transcription	NHDF-Ad	bronchial
10	chr16:69769800-69775000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr16:69770200-69778600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr16:69770400-69777400	Weak transcription	Right Ventricle	heart
13	chr16:69770400-69788000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr16:69770600-69775600	Weak transcription	Fetal Heart	heart
15	chr16:69770800-69775200	Weak transcription	Colonic Mucosa	Colon
16	chr16:69771200-69775200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr16:69771600-69775200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr16:69771600-69775200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr16:69771800-69777400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr16:69771800-69781400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr16:69771800-69786400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr16:69772600-69775000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr16:69772600-69786400	Strong transcription	Fetal Stomach	stomach
24	chr16:69772800-69786400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr16:69773000-69775200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr16:69773000-69775200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr16:69773000-69775200	Strong transcription	Fetal Intestine Large	intestine
28	chr16:69773000-69775200	Strong transcription	Fetal Intestine Small	intestine
29	chr16:69773000-69775400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr16:69773000-69775400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr16:69773000-69775400	Strong transcription	HUVEC	blood vessel
32	chr16:69773000-69775600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr16:69773000-69775600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr16:69773000-69775800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr16:69773000-69776000	Strong transcription	Fetal Muscle Trunk	muscle
36	chr16:69773000-69776200	Strong transcription	Left Ventricle	heart
37	chr16:69773000-69776800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr16:69773000-69781400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr16:69773000-69783000	Strong transcription	HepG2	liver
40	chr16:69773000-69783400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr16:69773000-69783400	Strong transcription	Primary T cells from cord blood	blood
42	chr16:69773000-69785600	Strong transcription	Stomach Smooth Muscle	stomach
43	chr16:69773000-69786000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr16:69773000-69786000	Strong transcription	Thymus	Thymus
45	chr16:69773000-69786200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr16:69773000-69786200	Strong transcription	Fetal Brain Female	brain
47	chr16:69773000-69786200	Strong transcription	Dnd41	blood
48	chr16:69773000-69786400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr16:69773000-69786600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr16:69773000-69786600	Strong transcription	Fetal Thymus	thymus

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