Variant report

Variant	rs10461079
Chromosome Location	chr4:8392724-8392725
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8389242..8391252-chr4:8392488..8394168,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1357481	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1880023	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs1880024	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1916326	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1949733	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2010758	0.81[ASN][1000 genomes]
rs2140337	0.91[EUR][1000 genomes]
rs2255501	0.81[EUR][1000 genomes]
rs2386227	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2631731	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631734	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631740	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2631743	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2631745	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2631754	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2631758	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2631762	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2688219	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2688223	0.91[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes]
rs2688224	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688227	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2688233	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2688235	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2688242	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2688243	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2688247	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3103067	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs3103069	0.89[EUR][1000 genomes]
rs3103071	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3103072	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3103099	0.88[EUR][1000 genomes]
rs4696828	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6447875	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6837429	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6845969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6858542	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs868105	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs871768	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs940133	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs940134	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs940136	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv878609	chr4:8373832-8407406	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv878610	chr4:8377058-8416976	ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	esv1005399	chr4:8387281-8397983	Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv470014	chr4:8390646-8429817	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10461079	TRMT44	cis	Nerve Tibial	GTEx
rs10461079	C4orf23	cis	brain	BrainEAC
rs10461079	ACOX3	Cis_1M	lymphoblastoid	RTeQTL
rs10461079	RP11-689P11.2	cis	lung	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8360400-8394000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:8360400-8395600	Weak transcription	NHEK	skin
3	chr4:8362000-8395400	Weak transcription	Fetal Brain Male	brain
4	chr4:8366400-8411600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:8373400-8401600	Strong transcription	Fetal Intestine Small	intestine
6	chr4:8375000-8401600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:8378600-8398600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:8378600-8398800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:8378800-8397800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:8379000-8395400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:8381000-8393800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:8381800-8394400	Strong transcription	Brain Germinal Matrix	brain
13	chr4:8381800-8398600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:8382400-8401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:8383800-8419000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:8384000-8394600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:8384000-8395600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:8384000-8399600	Strong transcription	Spleen	Spleen
19	chr4:8384800-8401600	Strong transcription	Thymus	Thymus
20	chr4:8384800-8418600	Strong transcription	Primary T cells from cord blood	blood
21	chr4:8385200-8395200	Weak transcription	Fetal Kidney	kidney
22	chr4:8385200-8411600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr4:8385400-8395600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:8385600-8407000	Weak transcription	Stomach Mucosa	stomach
25	chr4:8386000-8393400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:8386400-8393000	Strong transcription	Fetal Stomach	stomach
27	chr4:8386400-8398200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr4:8386400-8408400	Strong transcription	Fetal Intestine Large	intestine
29	chr4:8386600-8393400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:8386600-8398600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr4:8386600-8399400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr4:8386600-8400600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:8386800-8393000	Strong transcription	Adipose Nuclei	Adipose
34	chr4:8386800-8393000	Strong transcription	Rectal Smooth Muscle	rectum
35	chr4:8386800-8396600	Strong transcription	Lung	lung
36	chr4:8387000-8392800	Strong transcription	Brain Anterior Caudate	brain
37	chr4:8387200-8392800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:8387200-8394600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr4:8387200-8395000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:8387200-8395600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr4:8387400-8392800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:8387400-8393000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:8387400-8399600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr4:8387400-8412000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr4:8387600-8393400	Weak transcription	Right Atrium	heart
46	chr4:8387600-8394600	Strong transcription	Fetal Lung	lung
47	chr4:8387800-8393000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:8387800-8393600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr4:8388000-8393000	Weak transcription	NHDF-Ad	bronchial
50	chr4:8388000-8395000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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