Variant report

Variant	rs9347170
Chromosome Location	chr6:167405187-167405188
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:167370134..167371784-chr6:167403677..167406103,3	K562	blood:
2	chr6:167404788..167406294-chr6:167419141..167421789,2	K562	blood:
3	chr6:167369776..167371784-chr6:167403677..167406103,3	K562	blood:
4	chr6:167397805..167399426-chr6:167403364..167405935,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNASET2-5	chr6:167404676-167405315	NONHSAT116067

Variant related genes	Relation type
ENSG00000026297	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10946205	0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1130033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12055488	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13210649	0.87[ASN][1000 genomes]
rs162298	0.88[YRI][hapmap]
rs1951459	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204295	0.83[ASN][1000 genomes]
rs2181059	0.90[ASN][1000 genomes]
rs2237277	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2247314	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2247315	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2247325	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2282860	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2282861	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2285148	0.83[ASN][1000 genomes]
rs2345568	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs239933	0.96[ASN][1000 genomes]
rs2757039	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2757041	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2757053	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs393727	0.84[JPT][hapmap]
rs3963512	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs444210	0.97[ASN][1000 genomes]
rs4710149	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4710154	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4710176	0.82[ASN][1000 genomes]
rs6456143	0.96[ASN][1000 genomes]
rs6907666	0.91[CHB][hapmap]
rs6921588	0.83[ASN][1000 genomes]
rs6936261	0.87[ASN][1000 genomes]
rs6941355	0.80[ASN][1000 genomes]
rs7749278	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7750593	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs933243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9355610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9356551	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9457258	0.91[ASN][1000 genomes]
rs9459835	0.96[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9459842	0.89[ASN][1000 genomes]
rs9459853	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9347170	RNASET2	Cis_1M	lymphoblastoid	RTeQTL
rs9347170	AL133458.1	cis	Skin Sun Exposed Lower leg	GTEx
rs9347170	RNASET2	cis	Whole Blood	GTEx
rs9347170	RNASET2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167371400-167411000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:167381200-167410000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:167381200-167411000	Weak transcription	Fetal Stomach	stomach
4	chr6:167382000-167411200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:167383200-167411200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:167383400-167411000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:167384000-167410600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:167384000-167411000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:167384000-167411000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:167384400-167407400	Weak transcription	Fetal Intestine Large	intestine
11	chr6:167384400-167411000	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:167384600-167409600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr6:167385000-167411000	Weak transcription	Thymus	Thymus
14	chr6:167385400-167405800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:167385400-167411000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:167386200-167409400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr6:167388800-167410600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:167389600-167411000	Weak transcription	NHLF	lung
19	chr6:167390600-167411200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:167390800-167411000	Weak transcription	Gastric	stomach
21	chr6:167392200-167411000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:167392600-167410800	Weak transcription	HUVEC	blood vessel
23	chr6:167395200-167410200	Weak transcription	Fetal Lung	lung
24	chr6:167396800-167410800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:167398800-167411000	Weak transcription	Esophagus	oesophagus
26	chr6:167399400-167406000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr6:167400200-167408000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:167400400-167406000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:167400600-167405800	Weak transcription	Dnd41	blood
30	chr6:167401800-167411000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:167402000-167410800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:167402200-167410600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:167402400-167406000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:167402400-167406000	Weak transcription	K562	blood
35	chr6:167402600-167410000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:167402600-167411000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr6:167402600-167411000	Weak transcription	Fetal Intestine Small	intestine
38	chr6:167402600-167411200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:167402800-167405800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:167402800-167410800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:167402800-167411000	Weak transcription	NHEK	skin
42	chr6:167403000-167406000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:167403000-167408000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr6:167403000-167408200	Weak transcription	Fetal Thymus	thymus
45	chr6:167403000-167410800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:167403000-167411000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr6:167403000-167411000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:167403000-167411200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:167403200-167405800	Weak transcription	GM12878-XiMat	blood
50	chr6:167403200-167406000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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