Variant report

Variant	rs11120303
Chromosome Location	chr1:214537549-214537550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11120305	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs12059328	1.00[ASW][hapmap];0.87[CHB][hapmap]
rs12078216	0.84[CHB][hapmap]
rs12127760	1.00[MKK][hapmap]
rs12144357	1.00[MKK][hapmap]
rs12408452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1566249	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17022675	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17022757	0.87[CHB][hapmap];0.85[CHD][hapmap]
rs3738425	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]
rs4465172	1.00[ASW][hapmap]
rs4655249	1.00[ASW][hapmap]
rs4655339	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59017733	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59134396	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7532953	0.87[CHB][hapmap];0.85[CHD][hapmap]
rs7537274	1.00[ASW][hapmap]
rs7555415	1.00[ASW][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11120303	KCTD3	cis	parietal	SCAN
rs11120303	NEK2	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214503200-214537800	Weak transcription	Gastric	stomach
2	chr1:214513600-214552200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:214514000-214537800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:214515400-214542600	Weak transcription	Brain Substantia Nigra	brain
5	chr1:214518400-214537800	Weak transcription	Fetal Brain Male	brain
6	chr1:214519000-214557800	Weak transcription	Dnd41	blood
7	chr1:214519200-214577200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:214521200-214537600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:214522800-214552800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:214523400-214540800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:214524400-214574400	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:214524800-214537800	Strong transcription	NHEK	skin
13	chr1:214524800-214539200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:214525600-214540000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:214526000-214538600	Strong transcription	Stomach Smooth Muscle	stomach
16	chr1:214526000-214544600	Weak transcription	Spleen	Spleen
17	chr1:214526400-214542400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:214527400-214540600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:214527800-214542400	Weak transcription	HepG2	liver
20	chr1:214528600-214539800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:214528600-214552800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:214528600-214555800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:214528800-214538800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:214528800-214539200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:214528800-214551800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:214529000-214538400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:214529000-214584200	Weak transcription	Brain Anterior Caudate	brain
28	chr1:214529200-214539600	Strong transcription	Fetal Stomach	stomach
29	chr1:214529400-214561800	Weak transcription	Brain Angular Gyrus	brain
30	chr1:214529600-214537800	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr1:214529600-214544600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:214531600-214543400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:214531600-214556800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:214533000-214539200	Strong transcription	Fetal Lung	lung
35	chr1:214533200-214538400	Strong transcription	NHLF	lung
36	chr1:214533200-214538600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:214533400-214538800	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr1:214533600-214538600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:214534000-214538800	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr1:214534000-214557000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:214534200-214537800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:214534400-214537600	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:214534400-214538000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr1:214534800-214538200	Genic enhancers	HSMM	muscle
45	chr1:214534800-214538800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr1:214534800-214540400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:214535000-214537800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:214535000-214537800	Strong transcription	Colon Smooth Muscle	Colon
49	chr1:214535000-214537800	Strong transcription	Esophagus	oesophagus
50	chr1:214535000-214538400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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