Variant report

Variant	rs4419647
Chromosome Location	chr6:86225739-86225740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr6:86225735-86226349	ECC-1	luminal epithelium:	n/a	n/a
2	ARID3A	chr6:86225737-86226249	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SNX14	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1059306	0.90[EUR][1000 genomes]
rs10944133	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1173415	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12199873	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12205013	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1590281	0.81[ASN][1000 genomes]
rs1885607	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2065114	0.82[ASN][1000 genomes]
rs2208725	0.81[ASN][1000 genomes]
rs2229523	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2475790	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2475791	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2484355	0.82[EUR][1000 genomes]
rs2758840	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2758842	0.82[EUR][1000 genomes]
rs2758843	0.82[EUR][1000 genomes]
rs2758844	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2758846	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2758847	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2783171	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842601	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2842602	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2842604	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2842607	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2842608	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2842609	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2842612	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2842613	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2842614	0.82[EUR][1000 genomes]
rs2842617	0.82[EUR][1000 genomes]
rs3812133	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4145082	0.85[EUR][1000 genomes]
rs4235826	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4235827	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4282381	0.82[ASN][1000 genomes]
rs4304137	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4441928	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4501401	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4562107	0.81[ASN][1000 genomes]
rs4706240	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4707207	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4707209	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707217	0.81[EUR][1000 genomes]
rs6454468	0.82[ASN][1000 genomes]
rs6454469	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6454471	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6909767	0.87[EUR][1000 genomes]
rs6922	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6926049	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6931295	0.81[ASN][1000 genomes]
rs6935918	0.83[EUR][1000 genomes]
rs7452605	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7746065	0.81[ASN][1000 genomes]
rs7765636	0.81[ASN][1000 genomes]
rs7768065	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7770359	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7771612	0.84[EUR][1000 genomes]
rs7775864	0.84[EUR][1000 genomes]
rs911927	0.82[EUR][1000 genomes]
rs9294337	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9342041	0.83[EUR][1000 genomes]
rs9344532	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9344533	0.86[EUR][1000 genomes]
rs9351065	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9353318	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9353320	0.85[EUR][1000 genomes]
rs9362230	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9362233	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9444349	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9450272	0.81[ASN][1000 genomes]
rs9450290	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450302	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
14	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
15	esv1792638	chr6:86224053-86336300	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4419647	SNHG5	cis	multi-tissue	Pritchard
rs4419647	SNHG5	cis	Muscle Skeletal	GTEx
rs4419647	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs4419647	SNHG5	cis	Nerve Tibial	GTEx
rs4419647	SNHG5	cis	Heart Left Ventricle	GTEx
rs4419647	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs4419647	SNHG5	cis	Esophagus Mucosa	GTEx
rs4419647	SNHG5	cis	Esophagus Muscularis	GTEx
rs4419647	SNHG5	cis	Whole Blood	GTEx
rs4419647	SNHG5	cis	lung	GTEx
rs4419647	SNHG5	cis	Adipose Subcutaneous	GTEx
rs4419647	SNHG5	cis	Thyroid	GTEx
rs4419647	SNHG5	cis	Artery Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86176800-86242600	Weak transcription	Gastric	stomach
2	chr6:86207200-86238400	Weak transcription	Esophagus	oesophagus
3	chr6:86208800-86284600	Weak transcription	Small Intestine	intestine
4	chr6:86208800-86289200	Weak transcription	Pancreas	Pancrea
5	chr6:86211400-86246400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:86212000-86228600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr6:86212000-86246600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr6:86215800-86227600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:86218000-86260200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:86218400-86266200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:86218600-86226000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:86219200-86227600	Strong transcription	Duodenum Mucosa	Duodenum
13	chr6:86219200-86246200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr6:86219400-86227600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:86219600-86227600	Strong transcription	Dnd41	blood
16	chr6:86220200-86252400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:86220200-86257200	Weak transcription	Fetal Heart	heart
18	chr6:86221000-86245600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:86221400-86242800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:86221800-86285800	Weak transcription	Fetal Brain Male	brain
21	chr6:86222200-86232200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr6:86222200-86232400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:86222200-86249800	Weak transcription	Aorta	Aorta
24	chr6:86222400-86229200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:86222600-86229200	Weak transcription	Fetal Intestine Small	intestine
26	chr6:86222600-86233200	Weak transcription	Fetal Stomach	stomach
27	chr6:86222600-86243800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:86222600-86289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:86222800-86229600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:86223000-86242600	Weak transcription	Right Ventricle	heart
31	chr6:86223200-86231000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:86223200-86231000	Weak transcription	Ovary	ovary
33	chr6:86223200-86233200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:86223200-86235400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:86223200-86242200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:86223200-86242200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:86223200-86242600	Weak transcription	Psoas Muscle	Psoas
38	chr6:86223200-86242600	Weak transcription	Thymus	Thymus
39	chr6:86223200-86243000	Weak transcription	Brain Angular Gyrus	brain
40	chr6:86223200-86260200	Weak transcription	Lung	lung
41	chr6:86223400-86226400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:86223400-86227200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:86223400-86229000	Weak transcription	Fetal Intestine Large	intestine
44	chr6:86223400-86230200	Weak transcription	HSMMtube	muscle
45	chr6:86223400-86230400	Weak transcription	Fetal Lung	lung
46	chr6:86223400-86230800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:86223400-86231000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:86223400-86231600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr6:86223400-86231600	Weak transcription	Brain Hippocampus Middle	brain
50	chr6:86223400-86232000	Weak transcription	Fetal Kidney	kidney

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