Variant report

Variant	rs2769345
Chromosome Location	chr6:167366394-167366395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:167366051-167366485	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:167366148-167366432	HepG2	liver:	n/a	n/a
3	CHD1	chr6:167366372-167366428	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:167366100-167366837	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:167366333-167366950	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:167365398-167366859	GM12878	blood:	n/a	n/a
7	CHD2	chr6:167366219-167366443	GM12878	blood:	n/a	n/a
8	BHLHE40	chr6:167365579-167366412	GM12878	blood:	n/a	chr6:167365904-167365913
9	WRNIP1	chr6:167365988-167366907	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:167364990..167367805-chr6:167369090..167372947,3	K562	blood:

Variant related genes	Relation type
RNASET2	TF binding region
ENSG00000026297	Chromatin interaction
ENSG00000249141	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1819333	0.87[CEU][hapmap]
rs2149085	0.87[CEU][hapmap]
rs2149091	0.88[CEU][hapmap]
rs2149093	0.83[AMR][1000 genomes]
rs239935	0.87[CEU][hapmap];0.80[JPT][hapmap]
rs2757042	0.82[AMR][1000 genomes]
rs2769352	0.83[AMR][1000 genomes]
rs364451	0.81[AMR][1000 genomes]
rs385460	0.88[CEU][hapmap]
rs386548	0.87[CEU][hapmap]
rs387733	0.86[CEU][hapmap]
rs393727	0.89[CEU][hapmap]
rs400837	0.87[CEU][hapmap]
rs402191	0.95[CEU][hapmap]
rs405553	0.87[CEU][hapmap]
rs406095	0.85[CEU][hapmap]
rs408087	0.87[CEU][hapmap]
rs408918	0.87[CEU][hapmap]
rs409356	0.83[CEU][hapmap]
rs424185	0.83[CEU][hapmap]
rs425039	0.87[CEU][hapmap]
rs427824	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs429083	0.87[CEU][hapmap]
rs430097	0.88[CEU][hapmap]
rs430145	0.87[CEU][hapmap]
rs430293	0.88[CEU][hapmap]
rs433191	0.86[CEU][hapmap]
rs444988	0.81[AMR][1000 genomes]
rs448060	0.88[CEU][hapmap]
rs4710145	0.90[EUR][1000 genomes]
rs4710147	0.89[CEU][hapmap]
rs932644	0.87[CEU][hapmap]
rs9348211	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1019381	chr6:167090236-167558598	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv538541	chr6:167090236-167558598	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv948634	chr6:167200671-167838993	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
5	nsv482507	chr6:167282376-167474915	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv532074	chr6:167320656-167781977	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1031039	chr6:167324021-167741439	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv538543	chr6:167324021-167741439	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv1026972	chr6:167335031-167671042	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
10	nsv1034359	chr6:167359643-167384714	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2769345	RNASET2	cis	Whole Blood	GTEx
rs2769345	AL133458.1	cis	Whole Blood	GTEx
rs2769345	RNASET2	cis	Esophagus Mucosa	GTEx
rs2769345	RNASET2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167341000-167368800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:167341200-167368800	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:167342400-167368600	Weak transcription	Fetal Heart	heart
4	chr6:167344200-167368600	Weak transcription	Right Atrium	heart
5	chr6:167350600-167366400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:167350600-167367600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:167352200-167368800	Weak transcription	Fetal Kidney	kidney
8	chr6:167353800-167366600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:167354600-167368800	Weak transcription	HSMM	muscle
10	chr6:167354600-167369000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:167354600-167369000	Weak transcription	A549	lung
12	chr6:167356400-167366800	Strong transcription	Fetal Intestine Small	intestine
13	chr6:167360000-167368800	Weak transcription	Fetal Lung	lung
14	chr6:167360600-167368800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr6:167360600-167368800	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:167360600-167369000	Weak transcription	Osteobl	bone
17	chr6:167361200-167369000	Weak transcription	Ovary	ovary
18	chr6:167361200-167369200	Weak transcription	Aorta	Aorta
19	chr6:167361800-167368600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:167361800-167369000	Weak transcription	Psoas Muscle	Psoas
21	chr6:167362200-167368800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:167363000-167368000	Genic enhancers	Primary monocytes fromperipheralblood	blood
23	chr6:167363200-167366800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:167363200-167368000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
25	chr6:167363600-167368600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr6:167363600-167368800	Weak transcription	Brain Germinal Matrix	brain
27	chr6:167363800-167367600	Weak transcription	Small Intestine	intestine
28	chr6:167363800-167368800	Weak transcription	NHEK	skin
29	chr6:167364000-167366800	Strong transcription	Fetal Stomach	stomach
30	chr6:167364200-167367400	Weak transcription	Thymus	Thymus
31	chr6:167364200-167367800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:167364200-167368600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:167364200-167368600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:167364200-167368600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:167364200-167369000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:167364400-167366400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:167364400-167368600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:167364400-167368600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr6:167364400-167368600	Weak transcription	Esophagus	oesophagus
40	chr6:167364400-167368600	Weak transcription	Lung	lung
41	chr6:167364400-167368600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:167364400-167368600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:167364800-167368600	Genic enhancers	Primary B cells from peripheral blood	blood
44	chr6:167364800-167368800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:167364800-167369000	Weak transcription	Stomach Mucosa	stomach
46	chr6:167364800-167369200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr6:167365000-167366400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:167365000-167366400	Genic enhancers	Rectal Mucosa Donor 29	rectum
49	chr6:167365000-167367000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:167365000-167367600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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