Variant report

Variant	rs9450311
Chromosome Location	chr6:86376586-86376587
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	chr6:86350291..86355305-chr6:86366070..86378212,20	MCF-7	breast:
2	chr6:86294695..86297402-chr6:86376038..86378724,2	K562	blood:

Variant related genes	Relation type
ENSG00000135316	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 15 )

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

rs_ID	r²[population]
rs1059307	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10944128	0.80[EUR][1000 genomes]
rs10944129	0.80[EUR][1000 genomes]
rs1173416	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1173418	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11752795	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12193777	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12203963	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12206573	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2758848	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758849	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2842600	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2842605	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2842610	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842611	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2842615	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3087978	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34980280	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4348284	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4640862	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4707211	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4707212	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6454472	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6927475	0.82[EUR][1000 genomes]
rs7766485	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9342045	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9344540	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9362232	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9444351	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9444352	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444354	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450285	0.82[EUR][1000 genomes]
rs9450292	0.89[EUR][1000 genomes];0.85[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	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
2	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
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
4	nsv1028293	chr6:86353958-86778912	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases
5	nsv538350	chr6:86353958-86778912	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs9450311	SNHG5	cis	Artery Tibial	GTEx
rs9450311	SNHG5	cis	Whole Blood	GTEx
rs9450311	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs9450311	SNHG5	cis	multi-tissue	Pritchard
rs9450311	SNHG5	cis	Adipose Subcutaneous	GTEx
rs9450311	SNHG5	cis	lung	GTEx
rs9450311	SNHG5	cis	Stomach	GTEx
rs9450311	SNHG5	cis	Heart Left Ventricle	GTEx
rs9450311	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs9450311	SNHG5	cis	Thyroid	GTEx
rs9450311	SNHG5	cis	Esophagus Mucosa	GTEx
rs9450311	SNHG5	cis	Artery Aorta	GTEx
rs9450311	SNHG5	cis	Muscle Skeletal	GTEx
rs9450311	SNHG5	cis	Nerve Tibial	GTEx
rs9450311	SNHG5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86354600-86384200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:86355200-86377000	Weak transcription	Thymus	Thymus
3	chr6:86355200-86380400	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:86355400-86384400	Weak transcription	Pancreas	Pancrea
5	chr6:86366800-86377800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:86367800-86381800	Weak transcription	Lung	lung
7	chr6:86368200-86377600	Weak transcription	Primary T cells from cord blood	blood
8	chr6:86368200-86384800	Weak transcription	Right Ventricle	heart
9	chr6:86368600-86382600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:86368600-86384800	Weak transcription	Spleen	Spleen
11	chr6:86368800-86380200	Weak transcription	Adipose Nuclei	Adipose
12	chr6:86370200-86378200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:86370200-86379800	Weak transcription	Gastric	stomach
14	chr6:86370200-86384400	Weak transcription	Esophagus	oesophagus
15	chr6:86370200-86384400	Weak transcription	Fetal Brain Male	brain
16	chr6:86370200-86385200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:86370400-86380200	Weak transcription	Fetal Lung	lung
18	chr6:86370400-86382600	Weak transcription	A549	lung
19	chr6:86370400-86383200	Weak transcription	Aorta	Aorta
20	chr6:86370400-86384400	Weak transcription	Psoas Muscle	Psoas
21	chr6:86370400-86385200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:86370400-86386800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:86370600-86377800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:86370600-86379400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:86370600-86379600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:86370600-86379600	Weak transcription	Osteobl	bone
27	chr6:86370600-86379800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:86370600-86379800	Weak transcription	NHLF	lung
29	chr6:86370800-86384600	Weak transcription	HSMMtube	muscle
30	chr6:86371400-86377800	Strong transcription	Fetal Stomach	stomach
31	chr6:86371400-86383400	Weak transcription	Colon Smooth Muscle	Colon
32	chr6:86371800-86376800	Strong transcription	Fetal Muscle Leg	muscle
33	chr6:86372000-86379600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:86372200-86380400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:86373000-86384400	Weak transcription	Brain Anterior Caudate	brain
36	chr6:86373200-86377200	Strong transcription	Ovary	ovary
37	chr6:86373200-86381800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr6:86373400-86379200	Weak transcription	Primary B cells from cord blood	blood
39	chr6:86373400-86379200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:86373600-86382000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:86373800-86380200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr6:86374000-86385000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:86374200-86376800	Strong transcription	Fetal Intestine Small	intestine
44	chr6:86374200-86377400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr6:86374400-86377600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr6:86374400-86377600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:86374600-86381800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr6:86374600-86384400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr6:86374600-86385600	Weak transcription	Colonic Mucosa	Colon
50	chr6:86374800-86384800	Weak transcription	Rectal Mucosa Donor 31	rectum

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