Variant report

Variant	rs3738425
Chromosome Location	chr1:214543098-214543099
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11120303	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11120305	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs12059328	0.87[CHB][hapmap]
rs12078216	0.84[CHB][hapmap]
rs12408452	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1566249	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17022675	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17022757	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs1846251	0.82[ASN][1000 genomes]
rs4655339	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59017733	0.89[EUR][1000 genomes]
rs59134396	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7532953	0.87[CHB][hapmap];0.82[CHD][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3738425	KCTD3	cis	parietal	SCAN
rs3738425	NEK2	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214513600-214552200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:214519000-214557800	Weak transcription	Dnd41	blood
3	chr1:214519200-214577200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:214522800-214552800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:214524400-214574400	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:214526000-214544600	Weak transcription	Spleen	Spleen
7	chr1:214528600-214552800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:214528600-214555800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:214528800-214551800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:214529000-214584200	Weak transcription	Brain Anterior Caudate	brain
11	chr1:214529400-214561800	Weak transcription	Brain Angular Gyrus	brain
12	chr1:214529600-214544600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:214531600-214543400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:214531600-214556800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:214534000-214557000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:214536000-214545400	Strong transcription	NH-A	brain
17	chr1:214536200-214551000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:214537600-214545000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:214537600-214577000	Weak transcription	Stomach Mucosa	stomach
20	chr1:214537800-214543600	Weak transcription	Esophagus	oesophagus
21	chr1:214537800-214544800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:214537800-214547400	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:214537800-214549000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:214538000-214544000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:214538000-214544800	Weak transcription	Aorta	Aorta
26	chr1:214538000-214556200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:214538000-214556400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:214538000-214559400	Weak transcription	Small Intestine	intestine
29	chr1:214538200-214544000	Weak transcription	Gastric	stomach
30	chr1:214538200-214544000	Weak transcription	Left Ventricle	heart
31	chr1:214538200-214544600	Weak transcription	Fetal Heart	heart
32	chr1:214538200-214544800	Weak transcription	Right Ventricle	heart
33	chr1:214538200-214556600	Weak transcription	Pancreas	Pancrea
34	chr1:214538400-214545000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:214538600-214543200	Strong transcription	HSMMtube	muscle
36	chr1:214538600-214544600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:214538600-214544800	Weak transcription	Ovary	ovary
38	chr1:214538600-214544800	Strong transcription	Osteobl	bone
39	chr1:214538600-214546000	Weak transcription	Lung	lung
40	chr1:214538600-214550600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:214538800-214544800	Weak transcription	Psoas Muscle	Psoas
42	chr1:214538800-214549400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:214538800-214556400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:214539600-214544600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:214539600-214561600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:214539800-214551000	Strong transcription	NHDF-Ad	bronchial
47	chr1:214540200-214545200	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr1:214540200-214547600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:214540400-214548400	Strong transcription	NHEK	skin
50	chr1:214540400-214552000	Strong transcription	HUVEC	blood vessel

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