Variant report

Variant	rs3789699
Chromosome Location	chr1:95363001-95363002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:95357972..95361717-chr1:95362316..95366848,4	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11165272	0.84[EUR][1000 genomes]
rs11165274	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs12121091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12125005	0.81[EUR][1000 genomes]
rs12132647	0.84[EUR][1000 genomes]
rs12140798	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12747335	0.84[EUR][1000 genomes]
rs2275612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818929	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4847368	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs61772600	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859054	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3789699	CNN3	cis	parietal	SCAN
rs3789699	SLC44A3	cis	parietal	SCAN
rs3789699	BARHL2	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

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	chr1:95349800-95364200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:95350400-95368800	Weak transcription	Spleen	Spleen
5	chr1:95350400-95378200	Weak transcription	Brain Angular Gyrus	brain
6	chr1:95353400-95373600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:95353800-95363400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:95353800-95373600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:95354600-95367800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:95355000-95375200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:95355200-95373000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:95355800-95364400	Strong transcription	Fetal Intestine Large	intestine
13	chr1:95356000-95363400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:95356000-95363800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:95356000-95365400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:95356000-95370200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr1:95356000-95370800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr1:95356200-95375000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:95356400-95363800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:95356600-95364200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:95356600-95364200	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr1:95356600-95364200	Strong transcription	Osteobl	bone
23	chr1:95356800-95369000	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:95356800-95371400	Strong transcription	Liver	Liver
25	chr1:95357400-95364000	Strong transcription	NH-A	brain
26	chr1:95357800-95369000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:95357800-95390800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:95358400-95369200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:95358800-95363200	Weak transcription	Gastric	stomach
30	chr1:95358800-95363400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:95358800-95370600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:95359400-95370000	Weak transcription	Pancreas	Pancrea
33	chr1:95359600-95363400	Strong transcription	HSMM	muscle
34	chr1:95359600-95363600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr1:95359600-95366400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:95359600-95368800	Strong transcription	Left Ventricle	heart
37	chr1:95359800-95364200	Strong transcription	Rectal Smooth Muscle	rectum
38	chr1:95359800-95367800	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:95359800-95368600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:95359800-95369000	Strong transcription	NHDF-Ad	bronchial
41	chr1:95359800-95369200	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:95359800-95369200	Strong transcription	HUVEC	blood vessel
43	chr1:95359800-95369600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:95360000-95364600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:95360000-95366200	Strong transcription	Fetal Muscle Leg	muscle
46	chr1:95360000-95368400	Strong transcription	Placenta	Placenta
47	chr1:95360200-95363600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:95360200-95370200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:95360200-95373800	Weak transcription	Fetal Intestine Small	intestine
50	chr1:95360200-95375000	Weak transcription	Psoas Muscle	Psoas

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