Variant report

Variant	rs859054
Chromosome Location	chr1:95369211-95369212
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr1:95368674-95369690	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr1:95368786-95369589	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr1:95368809-95369671	SK-N-SH	brain:	n/a	n/a
4	MAFK	chr1:95368960-95369259	IMR90	lung:	n/a	chr1:95369133-95369142

Variant related genes	Relation type
CNN3	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11165274	1.00[CHB][hapmap]
rs12121091	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12140798	1.00[ASN][1000 genomes]
rs12144222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2275612	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2275613	1.00[ASN][1000 genomes]
rs3789699	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4847368	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs61772600	1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs859054	CNN3	cis	parietal	SCAN
rs859054	SLC44A3	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95329000-95385000	Weak transcription	Colonic Mucosa	Colon
2	chr1:95333200-95370000	Weak transcription	Small Intestine	intestine
3	chr1:95350400-95378200	Weak transcription	Brain Angular Gyrus	brain
4	chr1:95353400-95373600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:95353800-95373600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:95355000-95375200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:95355200-95373000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:95356000-95370200	Strong transcription	Fetal Muscle Trunk	muscle
9	chr1:95356000-95370800	Strong transcription	Duodenum Mucosa	Duodenum
10	chr1:95356200-95375000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:95356800-95371400	Strong transcription	Liver	Liver
12	chr1:95357800-95390800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:95358800-95370600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:95359400-95370000	Weak transcription	Pancreas	Pancrea
15	chr1:95359800-95369600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:95360200-95370200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:95360200-95373800	Weak transcription	Fetal Intestine Small	intestine
18	chr1:95360200-95375000	Weak transcription	Psoas Muscle	Psoas
19	chr1:95360400-95378400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:95360800-95369800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:95360800-95371200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:95360800-95373600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:95361000-95369600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:95361000-95369600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:95361000-95370800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:95361000-95371000	Strong transcription	HepG2	liver
27	chr1:95361400-95379600	Weak transcription	Esophagus	oesophagus
28	chr1:95363400-95372400	Genic enhancers	HSMM	muscle
29	chr1:95363600-95370000	Weak transcription	Aorta	Aorta
30	chr1:95363600-95377200	Weak transcription	Gastric	stomach
31	chr1:95363800-95370200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:95363800-95373000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:95364000-95371200	Genic enhancers	HSMMtube	muscle
34	chr1:95364000-95388600	Weak transcription	Fetal Brain Male	brain
35	chr1:95364400-95375000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:95364800-95384800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:95365000-95371000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr1:95365600-95375400	Weak transcription	Brain Germinal Matrix	brain
39	chr1:95366200-95369600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:95366400-95369400	Strong transcription	Fetal Stomach	stomach
41	chr1:95366600-95370000	Strong transcription	Fetal Muscle Leg	muscle
42	chr1:95367200-95371400	Genic enhancers	NH-A	brain
43	chr1:95367800-95369600	Enhancers	Rectal Smooth Muscle	rectum
44	chr1:95367800-95370000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:95367800-95370000	Weak transcription	Lung	lung
46	chr1:95367800-95370200	Weak transcription	Right Ventricle	heart
47	chr1:95367800-95371000	Genic enhancers	Muscle Satellite Cultured Cells	--
48	chr1:95367800-95371400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:95367800-95375600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:95367800-95376200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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