Variant report

Variant	rs6685963
Chromosome Location	chr1:209222499-209222500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10218724	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10863749	0.82[ASN][1000 genomes]
rs12037144	0.84[EUR][1000 genomes]
rs12037818	0.85[EUR][1000 genomes]
rs17013951	0.84[EUR][1000 genomes]
rs17013955	0.84[EUR][1000 genomes]
rs2093788	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2104309	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540499	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6666007	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6677861	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6689506	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6689873	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6698725	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6685963	SYT14	cis	parietal	SCAN
rs6685963	CR1	cis	cerebellum	SCAN
rs6685963	YOD1	cis	parietal	SCAN
rs6685963	LEMD1	cis	cerebellum	SCAN
rs6685963	PLEKHA6	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209213200-209224400	Weak transcription	Esophagus	oesophagus
2	chr1:209221000-209223400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:209221400-209223200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:209221600-209223600	Enhancers	HSMM	muscle
5	chr1:209221800-209222800	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:209221800-209223000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:209221800-209223000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:209221800-209223000	Enhancers	NH-A	brain
9	chr1:209221800-209223000	Enhancers	Osteobl	bone
10	chr1:209221800-209225600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:209222000-209222600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:209222000-209222600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:209222000-209222600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:209222000-209222600	Enhancers	Ovary	ovary
15	chr1:209222000-209222800	Enhancers	HMEC	breast
16	chr1:209222000-209223000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:209222000-209223000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:209222000-209223000	Enhancers	NHDF-Ad	bronchial
19	chr1:209222000-209223600	Enhancers	HSMMtube	muscle
20	chr1:209222000-209223800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:209222000-209225000	Enhancers	NHEK	skin
22	chr1:209222000-209225800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:209222200-209222600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:209222200-209222600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr1:209222200-209222600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:209222200-209222600	Enhancers	Fetal Stomach	stomach
27	chr1:209222200-209223000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:209222400-209222800	Enhancers	Fetal Muscle Leg	muscle
29	chr1:209222400-209223000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell

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