Variant report

Variant	rs2475791
Chromosome Location	chr6:86368164-86368165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86360455..86373602-chr6:86382637..86391992,19	MCF-7	breast:
2	chr6:86350291..86355305-chr6:86366070..86378212,20	MCF-7	breast:
3	chr6:86358964..86360482-chr6:86365980..86368680,2	K562	blood:

Variant related genes	Relation type
ENSG00000203875	Chromatin interaction
ENSG00000135316	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1059306	0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10944133	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1173415	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1173417	0.81[EUR][1000 genomes]
rs12199873	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12205013	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12212560	0.86[EUR][1000 genomes]
rs1885607	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2229523	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2475790	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2484355	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2758840	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758842	0.80[EUR][1000 genomes]
rs2758843	0.83[EUR][1000 genomes]
rs2758844	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2758845	0.85[EUR][1000 genomes]
rs2758846	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2758847	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783171	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842601	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842602	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842603	0.81[EUR][1000 genomes]
rs2842604	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842607	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842608	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2842609	0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2842612	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2842613	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2842614	0.80[EUR][1000 genomes]
rs2842617	0.80[EUR][1000 genomes]
rs3812133	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4145082	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4235826	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4235827	0.83[ASN][1000 genomes]
rs4304137	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4351223	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4383777	0.89[EUR][1000 genomes]
rs4419647	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4441928	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4501401	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4706240	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4707207	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4707209	0.81[ASN][1000 genomes]
rs4707217	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6454471	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6454486	0.89[EUR][1000 genomes]
rs6922	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs6926049	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7452605	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7742201	0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7746065	0.91[CHB][hapmap]
rs7752502	0.82[EUR][1000 genomes]
rs7757864	0.87[EUR][1000 genomes]
rs7762321	0.81[EUR][1000 genomes]
rs7768065	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs911927	0.83[EUR][1000 genomes]
rs9294337	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9342046	0.87[EUR][1000 genomes]
rs9344532	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9351065	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9353318	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9362230	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9362233	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9362239	0.90[EUR][1000 genomes]
rs9444349	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9450290	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450318	0.90[EUR][1000 genomes]
rs9450319	0.89[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2475791	SNHG5	cis	Muscle Skeletal	GTEx
rs2475791	SNHG5	cis	Thyroid	GTEx
rs2475791	SNHG5	cis	lung	GTEx
rs2475791	SNHG5	cis	Artery Tibial	GTEx
rs2475791	SNHG5	cis	Whole Blood	GTEx
rs2475791	SNHG5	cis	multi-tissue	Pritchard
rs2475791	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs2475791	SNHG5	cis	Adipose Subcutaneous	GTEx
rs2475791	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs2475791	SNHG5	cis	Esophagus Muscularis	GTEx
rs2475791	SNHG5	cis	Heart Left Ventricle	GTEx
rs2475791	SNHG5	cis	Nerve Tibial	GTEx
rs2475791	SNHG5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86354200-86374400	Weak transcription	Left Ventricle	heart
2	chr6:86354600-86369600	Weak transcription	Ovary	ovary
3	chr6:86354600-86372200	Weak transcription	Brain Anterior Caudate	brain
4	chr6:86354600-86384200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:86355200-86369800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:86355200-86377000	Weak transcription	Thymus	Thymus
7	chr6:86355200-86380400	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:86355400-86384400	Weak transcription	Pancreas	Pancrea
9	chr6:86355600-86369600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:86360000-86369800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:86360600-86375000	Weak transcription	Brain Germinal Matrix	brain
12	chr6:86364400-86369600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:86366800-86377800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr6:86367200-86369600	Weak transcription	Brain Substantia Nigra	brain
15	chr6:86367400-86368600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:86367400-86371400	Weak transcription	Fetal Stomach	stomach
17	chr6:86367400-86372000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:86367600-86369600	Weak transcription	Aorta	Aorta
19	chr6:86367600-86369800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:86367800-86368200	Active TSS	Primary T cells from cord blood	blood
21	chr6:86367800-86368200	ZNF genes & repeats	Fetal Muscle Leg	muscle
22	chr6:86367800-86371800	Weak transcription	Fetal Brain Female	brain
23	chr6:86367800-86375200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:86367800-86381800	Weak transcription	Lung	lung
25	chr6:86368000-86368200	ZNF genes & repeats	Right Ventricle	heart

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