Variant report

Variant	rs26075
Chromosome Location	chr5:179342960-179342961
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179337210..179339218-chr5:179341502..179344075,2	K562	blood:
2	chr5:179340989..179343245-chr5:179345713..179347574,2	MCF-7	breast:
3	chr5:179333320..179335912-chr5:179341952..179343944,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs152232	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs152233	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs152236	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152237	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152238	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs155574	0.84[EUR][1000 genomes]
rs155784	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs155795	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs155796	0.92[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs155797	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs156096	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs156101	0.80[EUR][1000 genomes]
rs156104	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs166032	0.80[GIH][hapmap]
rs1684973	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs182085	0.86[EUR][1000 genomes]
rs182086	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2431123	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2431124	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2434411	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs248217	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs248218	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs248219	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs248220	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs248222	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs248229	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs248230	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs248232	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs248252	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs26074	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	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs26078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs27410	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs27411	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs27471	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27474	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28325	0.82[EUR][1000 genomes]
rs30381	0.82[EUR][1000 genomes]
rs30382	0.82[EUR][1000 genomes]
rs30385	0.81[EUR][1000 genomes]
rs30386	0.91[MEX][hapmap]
rs32437	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs32438	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs32469	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs32470	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs32471	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs32472	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3734003	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs43155	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs457610	0.80[GIH][hapmap]
rs532795	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs574997	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs88183	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9957	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]

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
rs26075	BTNL3	cis	cerebellum	SCAN
rs26075	TBC1D9B	cis	Muscle Skeletal	GTEx
rs26075	C5orf45	cis	cerebellum	SCAN
rs26075	HIGD2A	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179335200-179343000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:179335200-179343600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:179335400-179344200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:179335400-179344400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:179335400-179344400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:179335400-179346400	Weak transcription	Brain Angular Gyrus	brain
7	chr5:179335400-179346600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:179335600-179344200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr5:179335800-179358200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:179336000-179344200	Weak transcription	Primary B cells from cord blood	blood
11	chr5:179336000-179346200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:179336000-179349000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:179336000-179361000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:179340800-179344400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:179341400-179343600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:179341400-179344400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:179341600-179343600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr5:179341600-179343600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr5:179341600-179344200	Weak transcription	Spleen	Spleen
20	chr5:179341600-179344200	Weak transcription	GM12878-XiMat	blood
21	chr5:179341600-179345800	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:179341600-179346800	Weak transcription	Fetal Thymus	thymus
23	chr5:179341800-179344200	Weak transcription	Placenta	Placenta
24	chr5:179342000-179343200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:179342000-179344200	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr5:179342000-179344200	Weak transcription	Brain Germinal Matrix	brain
27	chr5:179342000-179344200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr5:179342000-179344600	Weak transcription	Fetal Brain Female	brain
29	chr5:179342600-179343600	Enhancers	Fetal Brain Male	brain
30	chr5:179342600-179345000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:179342800-179343000	Enhancers	Fetal Muscle Leg	muscle
32	chr5:179342800-179343200	Enhancers	HSMMtube	muscle
33	chr5:179342800-179343400	Weak transcription	Primary B cells from peripheral blood	blood

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