Variant report

Variant	rs11752251
Chromosome Location	chr6:86162868-86162869
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	chr6:86160188..86163833-chr6:86163850..86166659,4	MCF-7	breast:
2	chr6:86159640..86161207-chr6:86161671..86163988,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135318	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10944128	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10944129	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12191637	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12193777	0.82[ASN][1000 genomes]
rs12203963	0.85[ASN][1000 genomes]
rs4288177	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4431401	0.93[ASN][1000 genomes]
rs4640862	0.82[ASN][1000 genomes]
rs4707211	0.82[ASN][1000 genomes]
rs4707212	0.82[ASN][1000 genomes]
rs6454472	0.85[ASN][1000 genomes]
rs6927475	0.91[ASN][1000 genomes]
rs9444348	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444351	0.82[ASN][1000 genomes]
rs9444352	0.80[ASN][1000 genomes]
rs9450273	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450277	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450285	0.90[ASN][1000 genomes]
rs9450292	0.82[ASN][1000 genomes]
rs9885944	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs11752251	SNHG5	cis	Whole Blood	GTEx
rs11752251	SNHG5	cis	Thyroid	GTEx
rs11752251	SNHG5	cis	Heart Left Ventricle	GTEx
rs11752251	SNHG5	cis	lung	GTEx
rs11752251	SNHG5	cis	Muscle Skeletal	GTEx
rs11752251	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs11752251	SNHG5	cis	multi-tissue	Pritchard
rs11752251	SNHG5	cis	Esophagus Muscularis	GTEx
rs11752251	NT5E	cis	Thyroid	GTEx
rs11752251	SNHG5	cis	Adipose Subcutaneous	GTEx
rs11752251	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs11752251	SNHG5	cis	Artery Aorta	GTEx
rs11752251	SNHG5	cis	Artery Tibial	GTEx
rs11752251	SNHG5	cis	Esophagus Mucosa	GTEx
rs11752251	SNHG5	cis	Nerve Tibial	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86160000-86164200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
2	chr6:86160600-86163000	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:86160600-86163000	Weak transcription	Right Ventricle	heart
4	chr6:86160600-86163600	Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr6:86160600-86163600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:86160600-86164600	Weak transcription	Pancreas	Pancrea
7	chr6:86160600-86168000	Weak transcription	Lung	lung
8	chr6:86160600-86171400	Weak transcription	Gastric	stomach
9	chr6:86160800-86167000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:86160800-86168000	Weak transcription	Esophagus	oesophagus
11	chr6:86161000-86164000	Enhancers	Duodenum Mucosa	Duodenum
12	chr6:86161200-86163600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr6:86161200-86164000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:86161200-86168600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:86161400-86163200	Flanking Active TSS	NH-A	brain
16	chr6:86161400-86163400	Flanking Active TSS	HepG2	liver
17	chr6:86161400-86164600	Transcr. at gene 5' and 3'	NHEK	skin
18	chr6:86161600-86163000	Enhancers	Stomach Mucosa	stomach
19	chr6:86161600-86163600	Enhancers	Colonic Mucosa	Colon
20	chr6:86161600-86163600	Enhancers	Small Intestine	intestine
21	chr6:86161600-86163600	Transcr. at gene 5' and 3'	HSMM	muscle
22	chr6:86161600-86164200	Transcr. at gene 5' and 3'	Osteobl	bone
23	chr6:86161600-86167000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:86161800-86163000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr6:86161800-86163200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr6:86161800-86163400	Enhancers	Fetal Stomach	stomach
27	chr6:86161800-86163600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:86161800-86166400	Weak transcription	Right Atrium	heart
29	chr6:86161800-86167600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:86161800-86170400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr6:86162000-86163000	Enhancers	Rectal Smooth Muscle	rectum
32	chr6:86162000-86163000	Flanking Active TSS	A549	lung
33	chr6:86162000-86163200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr6:86162000-86163200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr6:86162000-86163400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:86162000-86163600	Enhancers	Placenta	Placenta
37	chr6:86162000-86163800	Flanking Active TSS	GM12878-XiMat	blood
38	chr6:86162000-86164000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:86162000-86164000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:86162000-86164000	Enhancers	Aorta	Aorta
41	chr6:86162000-86166400	Weak transcription	Brain Anterior Caudate	brain
42	chr6:86162200-86163000	Weak transcription	Brain Angular Gyrus	brain
43	chr6:86162200-86163400	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr6:86162200-86164000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:86162400-86163400	Enhancers	Primary B cells from peripheral blood	blood
46	chr6:86162400-86163600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:86162400-86163600	Bivalent Enhancer	Adipose Nuclei	Adipose
48	chr6:86162400-86164200	Enhancers	Colon Smooth Muscle	Colon
49	chr6:86162400-86164400	Enhancers	Primary B cells from cord blood	blood
50	chr6:86162600-86163000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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