Variant report

Variant	rs4501401
Chromosome Location	chr6:86206396-86206397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86205630..86207293-chr6:86209333..86212533,3	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10944133	0.83[ASN][1000 genomes]
rs1173415	0.81[ASN][1000 genomes]
rs12199873	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12205013	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1590281	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1885607	0.84[AFR][1000 genomes]
rs2065114	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2208725	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2229523	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475790	0.83[ASN][1000 genomes]
rs2475791	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2758840	0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2758844	0.85[ASN][1000 genomes]
rs2758846	0.85[ASN][1000 genomes]
rs2758847	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2783171	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2842601	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2842602	0.85[ASN][1000 genomes]
rs2842604	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2842607	0.85[ASN][1000 genomes]
rs2842608	0.90[ASN][1000 genomes]
rs2842609	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2842612	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2842613	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3812133	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4235826	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4235827	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4282381	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4304137	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4419647	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4441928	0.94[ASN][1000 genomes]
rs4562107	0.82[ASN][1000 genomes]
rs4593336	0.81[EUR][1000 genomes]
rs4706240	0.91[ASN][1000 genomes]
rs4707207	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4707209	0.92[ASN][1000 genomes]
rs6454468	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6454469	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6454471	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6922	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926049	0.91[ASN][1000 genomes]
rs6931295	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7452605	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7739563	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7746065	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7765636	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7768065	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7770359	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9294337	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9344532	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9351065	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9353318	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9362230	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9362233	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9444349	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450272	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9450282	0.86[EUR][1000 genomes]
rs9450287	0.87[EUR][1000 genomes]
rs9450290	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
10	nsv886333	chr6:86199243-86289415	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv463939	chr6:86205323-86279737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv470839	chr6:86205323-86279737	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv604093	chr6:86205323-86279737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4501401	SNHG5	cis	Adipose Subcutaneous	GTEx
rs4501401	SNHG5	cis	Muscle Skeletal	GTEx
rs4501401	SNHG5	cis	lung	GTEx
rs4501401	SNHG5	cis	Esophagus Mucosa	GTEx
rs4501401	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs4501401	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs4501401	SNHG5	cis	Thyroid	GTEx
rs4501401	SNHG5	cis	Nerve Tibial	GTEx
rs4501401	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs4501401	SNHG5	cis	Artery Tibial	GTEx
rs4501401	SNHG5	cis	Whole Blood	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86176800-86242600	Weak transcription	Gastric	stomach
2	chr6:86178800-86206800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:86186800-86211000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:86192600-86207000	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:86192800-86221400	Weak transcription	Brain Substantia Nigra	brain
6	chr6:86193000-86221200	Weak transcription	A549	lung
7	chr6:86193200-86212200	Weak transcription	Brain Anterior Caudate	brain
8	chr6:86193400-86208600	Weak transcription	HUVEC	blood vessel
9	chr6:86193400-86219800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:86195000-86211800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:86195000-86219800	Weak transcription	Brain Angular Gyrus	brain
12	chr6:86196800-86206800	Weak transcription	Esophagus	oesophagus
13	chr6:86196800-86221600	Weak transcription	Spleen	Spleen
14	chr6:86199600-86219400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:86200000-86219200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:86200200-86219400	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:86200600-86206600	Weak transcription	Fetal Stomach	stomach
18	chr6:86200600-86207200	Strong transcription	Osteobl	bone
19	chr6:86200600-86207400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:86200600-86208800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:86200600-86220400	Weak transcription	Psoas Muscle	Psoas
22	chr6:86200600-86221800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:86200800-86206800	Weak transcription	NH-A	brain
24	chr6:86200800-86212800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:86201000-86216600	Weak transcription	Left Ventricle	heart
26	chr6:86201600-86218800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:86202600-86212000	Weak transcription	Primary T cells from cord blood	blood
28	chr6:86202800-86208400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:86202800-86211800	Weak transcription	Ovary	ovary
30	chr6:86202800-86218800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:86203000-86207000	Weak transcription	Aorta	Aorta
32	chr6:86203400-86219800	Weak transcription	NHLF	lung
33	chr6:86204800-86206400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:86204800-86207400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:86204800-86208000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:86204800-86208400	Weak transcription	NHEK	skin
37	chr6:86205000-86206800	Weak transcription	Fetal Muscle Leg	muscle
38	chr6:86205000-86207000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:86205000-86211000	Weak transcription	Adipose Nuclei	Adipose
40	chr6:86205000-86212400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:86205200-86206600	Weak transcription	Placenta	Placenta
42	chr6:86205200-86206800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:86205200-86207400	Strong transcription	HSMM	muscle
44	chr6:86205200-86208400	Weak transcription	Liver	Liver
45	chr6:86205200-86217600	Weak transcription	HSMMtube	muscle
46	chr6:86205200-86219600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr6:86205800-86208200	Weak transcription	HMEC	breast
48	chr6:86206000-86206800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:86206000-86206800	Weak transcription	Fetal Intestine Large	intestine
50	chr6:86206000-86207200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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