Variant report

Variant	rs16971465
Chromosome Location	chr16:73017061-73017062
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:73015896..73018125-chr16:73080034..73081873,2	MCF-7	breast:
2	chr16:73009955..73011584-chr16:73014836..73017573,2	MCF-7	breast:
3	chr16:73015247..73017675-chr16:73019626..73021160,2	MCF-7	breast:
4	chr16:73011122..73013946-chr16:73015634..73017223,2	MCF-7	breast:
5	chr16:72987849..72990412-chr16:73015041..73018020,2	MCF-7	breast:

Extended variants
information (count: 7 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11640395	1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2040507	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs55810200	0.98[ASN][1000 genomes]
rs56404375	0.96[ASN][1000 genomes]
rs73594707	0.94[ASN][1000 genomes]
rs9927735	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9937546	1.00[JPT][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16971465	SMPD1	trans	lymphoblastoid	seeQTL
rs16971465	FTSJD1	cis	parietal	SCAN
rs16971465	AP1G1	cis	cerebellum	SCAN
rs16971465	NRN1L	cis	cerebellum	SCAN
rs16971465	VAC14	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72993400-73019600	Weak transcription	Hela-S3	cervix
2	chr16:72993600-73019000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr16:72996200-73017800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr16:72996800-73018800	Weak transcription	NHLF	lung
5	chr16:72997000-73017800	Weak transcription	HSMMtube	muscle
6	chr16:72998400-73018800	Weak transcription	Osteobl	bone
7	chr16:73001200-73019000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr16:73002200-73019000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr16:73003000-73018000	Weak transcription	Brain Substantia Nigra	brain
10	chr16:73003200-73018800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr16:73003400-73017600	Weak transcription	HSMM	muscle
12	chr16:73003800-73019000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr16:73005000-73019400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr16:73005600-73017600	Weak transcription	Brain Anterior Caudate	brain
15	chr16:73007000-73018400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr16:73007400-73017400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr16:73007400-73019600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr16:73008600-73019000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr16:73008800-73023000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr16:73010800-73017800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr16:73011200-73017800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr16:73011200-73018000	Weak transcription	Stomach Mucosa	stomach
23	chr16:73011400-73017800	Weak transcription	Fetal Intestine Large	intestine
24	chr16:73011400-73018800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr16:73011400-73019000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr16:73011600-73019000	Weak transcription	Fetal Heart	heart
27	chr16:73012000-73019000	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr16:73012400-73019000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr16:73012600-73017600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr16:73012600-73017800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr16:73012600-73018600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr16:73012800-73020000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr16:73012800-73020400	Weak transcription	Fetal Intestine Small	intestine
34	chr16:73012800-73023400	Weak transcription	A549	lung
35	chr16:73013000-73017600	Weak transcription	Esophagus	oesophagus
36	chr16:73013000-73018600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr16:73013200-73017400	Weak transcription	Pancreas	Pancrea
38	chr16:73013200-73017600	Weak transcription	Right Atrium	heart
39	chr16:73013200-73017800	Weak transcription	Spleen	Spleen
40	chr16:73013200-73018800	Weak transcription	Adipose Nuclei	Adipose
41	chr16:73013200-73019000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr16:73013200-73023400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr16:73013200-73023600	Weak transcription	Small Intestine	intestine
44	chr16:73014800-73019400	Weak transcription	Liver	Liver
45	chr16:73015200-73026200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr16:73015400-73017600	Weak transcription	Fetal Lung	lung
47	chr16:73015600-73017800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr16:73015600-73019000	Weak transcription	Brain Germinal Matrix	brain
49	chr16:73015600-73019000	Weak transcription	Fetal Brain Female	brain
50	chr16:73015800-73019600	Weak transcription	Ovary	ovary

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