Variant report

Variant	rs1173415
Chromosome Location	chr6:86374226-86374227
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	POLR2A	chr6:86370760-86381789	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86350291..86355305-chr6:86366070..86378212,20	MCF-7	breast:
2	chr6:86369831..86371356-chr6:86373551..86376198,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NT5E-2	chr6:86371217-86374239	NONHSAT113850

Variant related genes	Relation type
PKMP3	TF binding region
ENSG00000220563	Chromatin interaction
ENSG00000135316	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1059306	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10944133	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12199873	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12205013	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12212560	0.82[EUR][1000 genomes]
rs1885607	0.86[EUR][1000 genomes]
rs2229523	0.81[ASN][1000 genomes]
rs2475790	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2475791	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2484355	0.87[EUR][1000 genomes]
rs2758840	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2758843	0.81[EUR][1000 genomes]
rs2758844	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758845	0.81[EUR][1000 genomes]
rs2758846	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758847	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2783171	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2842601	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842602	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842604	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842607	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842608	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2842609	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2842612	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2842613	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3812133	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4145082	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4235827	0.81[ASN][1000 genomes]
rs4383777	0.85[EUR][1000 genomes]
rs4419647	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4441928	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4501401	0.81[ASN][1000 genomes]
rs4706240	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4707217	0.85[EUR][1000 genomes]
rs6454471	0.81[ASN][1000 genomes]
rs6454486	0.85[EUR][1000 genomes]
rs6922	0.81[ASN][1000 genomes]
rs6926049	0.85[ASN][1000 genomes]
rs7452605	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7742201	0.86[EUR][1000 genomes]
rs7757864	0.84[EUR][1000 genomes]
rs7768065	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs911927	0.81[EUR][1000 genomes]
rs9294337	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9342046	0.83[EUR][1000 genomes]
rs9344532	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9351065	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9353318	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9362230	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9362233	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9362239	0.86[EUR][1000 genomes]
rs9444349	0.81[ASN][1000 genomes]
rs9450290	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9450318	0.86[EUR][1000 genomes]
rs9450319	0.85[EUR][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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1173415	SNHG5	cis	Artery Tibial	GTEx
rs1173415	SNHG5	cis	Whole Blood	GTEx
rs1173415	SNHG5	cis	Adipose Subcutaneous	GTEx
rs1173415	SNHG5	cis	Nerve Tibial	GTEx
rs1173415	SNHG5	cis	Heart Left Ventricle	GTEx
rs1173415	SNHG5	cis	Thyroid	GTEx
rs1173415	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs1173415	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs1173415	SNHG5	cis	Esophagus Muscularis	GTEx
rs1173415	SNHG5	cis	Esophagus Mucosa	GTEx
rs1173415	SNHG5	cis	lung	GTEx
rs1173415	SNHG5	cis	Muscle Skeletal	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86354200-86374400	Weak transcription	Left Ventricle	heart
2	chr6:86354600-86384200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:86355200-86377000	Weak transcription	Thymus	Thymus
4	chr6:86355200-86380400	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:86355400-86384400	Weak transcription	Pancreas	Pancrea
6	chr6:86360600-86375000	Weak transcription	Brain Germinal Matrix	brain
7	chr6:86366800-86377800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:86367800-86375200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:86367800-86381800	Weak transcription	Lung	lung
10	chr6:86368200-86377600	Weak transcription	Primary T cells from cord blood	blood
11	chr6:86368200-86384800	Weak transcription	Right Ventricle	heart
12	chr6:86368400-86374400	Weak transcription	Fetal Thymus	thymus
13	chr6:86368400-86375000	Weak transcription	Fetal Intestine Large	intestine
14	chr6:86368600-86382600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:86368600-86384800	Weak transcription	Spleen	Spleen
16	chr6:86368800-86380200	Weak transcription	Adipose Nuclei	Adipose
17	chr6:86370200-86375000	Weak transcription	Brain Substantia Nigra	brain
18	chr6:86370200-86378200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:86370200-86379800	Weak transcription	Gastric	stomach
20	chr6:86370200-86384400	Weak transcription	Esophagus	oesophagus
21	chr6:86370200-86384400	Weak transcription	Fetal Brain Male	brain
22	chr6:86370200-86385200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:86370400-86375000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:86370400-86375000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:86370400-86375000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:86370400-86375000	Weak transcription	Brain Angular Gyrus	brain
27	chr6:86370400-86375000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:86370400-86380200	Weak transcription	Fetal Lung	lung
29	chr6:86370400-86382600	Weak transcription	A549	lung
30	chr6:86370400-86383200	Weak transcription	Aorta	Aorta
31	chr6:86370400-86384400	Weak transcription	Psoas Muscle	Psoas
32	chr6:86370400-86385200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:86370400-86386800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:86370600-86377800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:86370600-86379400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:86370600-86379600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:86370600-86379600	Weak transcription	Osteobl	bone
38	chr6:86370600-86379800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:86370600-86379800	Weak transcription	NHLF	lung
40	chr6:86370800-86384600	Weak transcription	HSMMtube	muscle
41	chr6:86371400-86377800	Strong transcription	Fetal Stomach	stomach
42	chr6:86371400-86383400	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:86371600-86376400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:86371800-86375000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:86371800-86375800	Strong transcription	Fetal Brain Female	brain
46	chr6:86371800-86376800	Strong transcription	Fetal Muscle Leg	muscle
47	chr6:86372000-86379600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:86372200-86380400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:86372400-86375000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:86372800-86374800	Weak transcription	Liver	Liver

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