Variant report

Variant	rs1546550
Chromosome Location	chr12:26222745-26222746
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10842669	0.83[EUR][1000 genomes]
rs2048609	0.90[EUR][1000 genomes]
rs2271480	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2620705	0.83[EUR][1000 genomes]
rs2669563	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2669564	0.90[EUR][1000 genomes]
rs2669565	0.95[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2669566	0.95[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2669567	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2729626	0.95[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4963952	0.95[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs7132288	0.83[EUR][1000 genomes]
rs7306344	0.87[EUR][1000 genomes]
rs7961722	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs885208	0.86[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs9804762	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv973038	chr12:26221928-26224398	Strong transcription Weak transcription Enhancers Genic enhancers	lncRNA miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1546550	KLHDC5	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26192400-26228600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:26197200-26228600	Weak transcription	Aorta	Aorta
3	chr12:26200800-26229000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:26201000-26223400	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:26201200-26234600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:26201600-26236200	Weak transcription	Right Ventricle	heart
7	chr12:26206800-26229600	Weak transcription	Ovary	ovary
8	chr12:26206800-26229800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:26207400-26223600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:26207800-26224000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:26207800-26224000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:26208400-26234600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:26209600-26224800	Weak transcription	Brain Anterior Caudate	brain
14	chr12:26209600-26230400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:26211400-26227400	Weak transcription	Placenta	Placenta
16	chr12:26211600-26223800	Weak transcription	Fetal Intestine Large	intestine
17	chr12:26211600-26234600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:26211800-26230800	Weak transcription	Fetal Lung	lung
19	chr12:26212200-26223400	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:26214400-26224800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:26215200-26230200	Weak transcription	Adipose Nuclei	Adipose
22	chr12:26215800-26230800	Weak transcription	A549	lung
23	chr12:26216000-26226800	Weak transcription	Hela-S3	cervix
24	chr12:26216000-26227600	Weak transcription	HSMMtube	muscle
25	chr12:26216000-26228800	Weak transcription	HSMM	muscle
26	chr12:26216000-26229200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:26216000-26230400	Weak transcription	Psoas Muscle	Psoas
28	chr12:26216000-26230600	Weak transcription	HMEC	breast
29	chr12:26216000-26230800	Weak transcription	NHLF	lung
30	chr12:26216000-26231000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:26216200-26230800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:26216200-26231000	Weak transcription	NH-A	brain
33	chr12:26216400-26223400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:26217000-26226200	Strong transcription	NHDF-Ad	bronchial
35	chr12:26217800-26223400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:26218200-26224000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:26218200-26224000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:26219800-26224000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:26220200-26222800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:26220200-26223200	Strong transcription	Osteobl	bone
41	chr12:26220600-26227600	Weak transcription	Fetal Kidney	kidney
42	chr12:26220800-26225000	Weak transcription	Brain Substantia Nigra	brain
43	chr12:26221600-26222800	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr12:26221800-26223400	Weak transcription	Lung	lung
45	chr12:26221800-26224400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:26221800-26226200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:26221800-26230800	Weak transcription	Fetal Stomach	stomach
48	chr12:26221800-26234000	Weak transcription	Fetal Intestine Small	intestine
49	chr12:26222000-26224800	Weak transcription	Brain Hippocampus Middle	brain
50	chr12:26222000-26228000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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