Variant report

Variant	rs9444348
Chromosome Location	chr6:86175574-86175575
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	chr6:86159467..86161013-chr6:86173619..86175929,2	K562	blood:

Variant related genes	Relation type
ENSG00000135318	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10944128	0.81[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10944129	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11752251	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11752795	0.81[ASN][1000 genomes]
rs12191637	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12193777	0.84[ASN][1000 genomes]
rs12203963	0.87[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs12206573	0.82[ASN][1000 genomes]
rs2758848	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2842600	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2842611	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs4288177	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4348284	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs4431401	0.91[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4640862	0.84[ASN][1000 genomes]
rs4707211	0.87[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4707212	0.84[ASN][1000 genomes]
rs6454472	0.86[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs6927475	0.93[ASN][1000 genomes]
rs7766485	0.86[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs9444351	0.84[ASN][1000 genomes]
rs9444352	0.86[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs9444354	0.81[ASN][1000 genomes]
rs9450273	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9450277	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450285	0.91[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs9450288	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs9450292	0.84[ASN][1000 genomes]
rs9885944	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[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	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking 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	136 gene(s)	inside rSNPs	diseases
5	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv520112	chr6:86144875-86247759	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs9444348	NT5E	cis	Thyroid	GTEx
rs9444348	C6orf160	cis	normal skin	skin_eQTL
rs9444348	SNHG5	cis	Whole Blood	GTEx
rs9444348	SNHG5	cis	Adipose Subcutaneous	GTEx
rs9444348	SNHG5	cis	lung	GTEx
rs9444348	SNHG5	cis	Nerve Tibial	GTEx
rs9444348	SNHG5	cis	Esophagus Mucosa	GTEx
rs9444348	SNHG5	cis	Heart Left Ventricle	GTEx
rs9444348	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs9444348	SNHG5	cis	multi-tissue	Pritchard
rs9444348	SNHG5	cis	Artery Aorta	GTEx
rs9444348	SNHG5	cis	Muscle Skeletal	GTEx
rs9444348	SNHG5	cis	Esophagus Muscularis	GTEx
rs9444348	C6orf160	cis	lesional skin	skin_eQTL
rs9444348	C6orf160	cis	uninvolved skin	skin_eQTL
rs9444348	SNHG5	cis	Thyroid	GTEx
rs9444348	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs9444348	SNHG5	cis	Artery Tibial	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86163200-86176600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr6:86167800-86176200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:86171800-86176800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:86171800-86185200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:86171800-86186000	Weak transcription	Fetal Stomach	stomach
6	chr6:86171800-86187600	Weak transcription	Colonic Mucosa	Colon
7	chr6:86172000-86179000	Weak transcription	Pancreas	Pancrea
8	chr6:86172200-86179800	Weak transcription	Left Ventricle	heart
9	chr6:86172200-86186000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:86172400-86176200	Enhancers	Primary T cells from cord blood	blood
11	chr6:86172400-86178000	Weak transcription	Aorta	Aorta
12	chr6:86172400-86192800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:86173200-86176200	Enhancers	GM12878-XiMat	blood
14	chr6:86173400-86175600	Enhancers	Primary hematopoietic stem cells	blood
15	chr6:86173400-86176000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:86173600-86175600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr6:86174000-86175600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:86174000-86175800	Enhancers	Spleen	Spleen
19	chr6:86174000-86176600	Enhancers	Placenta	Placenta
20	chr6:86174200-86175600	Enhancers	Colon Smooth Muscle	Colon
21	chr6:86174200-86175600	Enhancers	Ovary	ovary
22	chr6:86174200-86175600	Enhancers	Stomach Smooth Muscle	stomach
23	chr6:86174200-86175800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:86174200-86176000	Enhancers	Esophagus	oesophagus
25	chr6:86174200-86176200	Weak transcription	Liver	Liver
26	chr6:86174200-86177000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr6:86174400-86176000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr6:86174400-86176000	Weak transcription	Gastric	stomach
29	chr6:86174400-86176200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:86174400-86176200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:86174600-86175600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr6:86174600-86175800	Enhancers	Osteobl	bone
33	chr6:86174600-86176000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:86174600-86176000	Enhancers	HMEC	breast
35	chr6:86174600-86176200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:86174600-86178600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:86174600-86180200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:86174800-86175800	Weak transcription	HepG2	liver
39	chr6:86174800-86176000	Enhancers	NHDF-Ad	bronchial
40	chr6:86174800-86176200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr6:86174800-86178000	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:86174800-86179800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:86174800-86180400	Weak transcription	Brain Anterior Caudate	brain
44	chr6:86175000-86175600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:86175000-86175600	Enhancers	HSMMtube	muscle
46	chr6:86175000-86176000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:86175000-86176000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:86175000-86176200	Enhancers	A549	lung
49	chr6:86175000-86180000	Genic enhancers	HSMM	muscle
50	chr6:86175200-86175800	Weak transcription	Fetal Thymus	thymus

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