Variant report

Variant	rs469318
Chromosome Location	chr5:179340006-179340007
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	chr5:179327650..179329496-chr5:179338121..179340094,2	MCF-7	breast:
3	chr5:179305999..179308737-chr5:179338946..179340504,2	MCF-7	breast:
4	chr5:179333591..179336519-chr5:179336661..179341628,9	MCF-7	breast:
5	chr5:179333496..179336752-chr5:179337888..179342042,8	K562	blood:
6	chr5:179339541..179342239-chr5:179346452..179348060,2	K562	blood:

Variant related genes	Relation type
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10491478	0.82[CEU][hapmap]
rs13164817	1.00[YRI][hapmap]
rs248216	1.00[YRI][hapmap]
rs9957	1.00[YRI][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs469318	TBC1D9B	cis	Muscle Skeletal	GTEx
rs469318	BTNL3	cis	cerebellum	SCAN
rs469318	CANX	cis	parietal	SCAN
rs469318	SNORD95	cis	parietal	SCAN
rs469318	HIGD2A	cis	cerebellum	SCAN
rs469318	SLC34A1	cis	parietal	SCAN
rs469318	LTC4S	cis	cerebellum	SCAN

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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