Variant report

Variant	rs26077
Chromosome Location	chr5:179340137-179340138
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179339757..179341423-chr5:179384531..179387426,2	MCF-7	breast:
2	chr5:179305999..179308737-chr5:179338946..179340504,2	MCF-7	breast:
3	chr5:179333591..179336519-chr5:179336661..179341628,9	MCF-7	breast:
4	chr5:179333496..179336752-chr5:179337888..179342042,8	K562	blood:
5	chr5:179339541..179342239-chr5:179346452..179348060,2	K562	blood:

Variant related genes	Relation type
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs152232	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs152233	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs152236	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs152237	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs152238	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs155784	0.81[ASN][1000 genomes]
rs155795	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs155796	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs155797	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs156096	0.81[EUR][1000 genomes]
rs156104	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1684973	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs182085	0.81[EUR][1000 genomes]
rs182086	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2431123	0.80[EUR][1000 genomes]
rs2431124	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2434411	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs248218	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs248219	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs248222	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs248229	0.81[ASN][1000 genomes]
rs248232	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs248252	0.81[ASN][1000 genomes]
rs26074	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs26075	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs26078	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs27410	0.83[EUR][1000 genomes]
rs27411	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27471	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27474	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30381	0.81[ASN][1000 genomes]
rs30382	0.81[ASN][1000 genomes]
rs32437	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32438	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32469	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs32470	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs32471	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs32472	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3734003	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs43155	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs532795	0.81[ASN][1000 genomes]
rs574997	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs860706	0.81[ASN][1000 genomes]
rs88183	0.82[EUR][1000 genomes];0.82[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs26077	TBC1D9B	cis	Muscle Skeletal	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

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	chr5:179335400-179340800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:179335400-179344200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:179335400-179344400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:179335400-179344400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:179335400-179346400	Weak transcription	Brain Angular Gyrus	brain
8	chr5:179335400-179346600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:179335600-179340600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:179335600-179340800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:179335600-179344200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:179335800-179340400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:179335800-179340800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:179335800-179340800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:179335800-179340800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr5:179335800-179340800	Weak transcription	Osteobl	bone
17	chr5:179335800-179341000	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr5:179335800-179341000	Weak transcription	Brain Substantia Nigra	brain
19	chr5:179335800-179358200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr5:179336000-179340600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:179336000-179340600	Weak transcription	Fetal Muscle Leg	muscle
22	chr5:179336000-179340800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:179336000-179341000	Weak transcription	Lung	lung
24	chr5:179336000-179344200	Weak transcription	Primary B cells from cord blood	blood
25	chr5:179336000-179346200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:179336000-179349000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr5:179336000-179361000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:179336200-179340400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr5:179336200-179340600	Weak transcription	Spleen	Spleen
30	chr5:179336200-179340800	Weak transcription	Placenta	Placenta
31	chr5:179336200-179341000	Weak transcription	Adipose Nuclei	Adipose
32	chr5:179336400-179340800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr5:179336600-179341000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr5:179339200-179341800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr5:179339400-179340600	Enhancers	NHEK	skin
36	chr5:179339400-179340800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr5:179339400-179340800	Enhancers	Stomach Mucosa	stomach
38	chr5:179339400-179340800	Enhancers	Stomach Smooth Muscle	stomach
39	chr5:179339400-179341600	Enhancers	Gastric	stomach
40	chr5:179339400-179342000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr5:179339400-179342000	Strong transcription	Brain Germinal Matrix	brain
42	chr5:179339600-179340200	Enhancers	Brain Hippocampus Middle	brain
43	chr5:179339600-179340200	Enhancers	Fetal Brain Female	brain
44	chr5:179339600-179340800	Enhancers	Fetal Brain Male	brain
45	chr5:179339600-179341600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:179339600-179341600	Enhancers	Esophagus	oesophagus
47	chr5:179339800-179340800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr5:179339800-179340800	Enhancers	HSMMtube	muscle
49	chr5:179339800-179341000	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr5:179339800-179341600	Enhancers	HMEC	breast

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