Variant report

Variant	rs26074
Chromosome Location	chr5:179345996-179345997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179344667..179348658-chr5:179348694..179351891,3	MCF-7	breast:
2	chr5:179334067..179337009-chr5:179345090..179348223,4	MCF-7	breast:
3	chr5:179340989..179343245-chr5:179345713..179347574,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF130-1	chr5:179345911-179347229	NONHSAT105657

Variant related genes	Relation type
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs152232	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs152233	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs152236	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs152237	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs152238	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs155574	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs155784	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs155795	0.84[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs155796	0.84[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs155797	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs156096	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs156104	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs166032	0.86[ASW][hapmap];0.84[CEU][hapmap]
rs1684973	0.88[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs182085	0.89[EUR][1000 genomes]
rs182086	0.84[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2431123	0.88[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2431124	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs2434411	0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]
rs248217	0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs248218	0.93[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs248219	0.88[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs248220	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap]
rs248222	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248229	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248230	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs248232	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248252	0.88[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs26075	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26077	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs26078	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs27410	0.88[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27411	0.93[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27471	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27474	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28325	0.81[ASN][1000 genomes]
rs30381	0.82[ASN][1000 genomes]
rs30382	0.82[ASN][1000 genomes]
rs30385	0.81[ASN][1000 genomes]
rs30386	0.84[CHD][hapmap];0.91[MEX][hapmap]
rs32437	0.84[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs32438	0.88[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs32469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32470	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32471	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs32472	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3734003	0.88[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs43155	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs456958	0.83[CEU][hapmap]
rs457610	0.86[ASW][hapmap];0.84[CEU][hapmap];0.80[GIH][hapmap]
rs464219	0.84[CEU][hapmap]
rs467764	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs518075	0.86[ASW][hapmap];0.84[CEU][hapmap]
rs532795	0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]
rs574997	0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs860706	0.82[ASN][1000 genomes]
rs88183	0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9957	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
3	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
4	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
6	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
7	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs26074	BTNL3	cis	cerebellum	SCAN
rs26074	TBC1D9B	cis	Muscle Skeletal	GTEx
rs26074	HIGD2A	cis	cerebellum	SCAN
rs26074	C5orf45	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179335400-179346400	Weak transcription	Brain Angular Gyrus	brain
2	chr5:179335400-179346600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:179335800-179358200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:179336000-179346200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:179336000-179349000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:179336000-179361000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:179341600-179346800	Weak transcription	Fetal Thymus	thymus
8	chr5:179343000-179348000	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:179344200-179347400	Strong transcription	Brain Germinal Matrix	brain
10	chr5:179344400-179347000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:179344600-179346400	Weak transcription	Fetal Stomach	stomach
12	chr5:179344600-179347600	Strong transcription	Fetal Brain Female	brain
13	chr5:179344600-179381600	Weak transcription	Fetal Brain Male	brain
14	chr5:179344800-179346600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:179344800-179346600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:179344800-179350400	Weak transcription	Primary B cells from cord blood	blood
17	chr5:179344800-179350400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr5:179344800-179351400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:179345000-179346200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:179345000-179346200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr5:179345000-179346400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr5:179345000-179347000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr5:179345000-179350200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr5:179345000-179350400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr5:179345400-179346000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:179345400-179347200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr5:179345800-179347400	Strong transcription	Brain Hippocampus Middle	brain

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