Variant report

Variant	rs11915970
Chromosome Location	chr3:56169965-56169966
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1078309	0.86[JPT][hapmap]
rs1078310	0.86[JPT][hapmap]
rs1376984	0.92[CHB][hapmap]
rs1564907	0.82[ASN][1000 genomes]
rs2176637	0.86[ASN][1000 genomes]
rs4974170	0.83[ASN][1000 genomes]
rs4974171	0.81[ASN][1000 genomes]
rs4974173	0.90[CHB][hapmap]
rs6445770	1.00[CHB][hapmap]
rs6764295	0.92[CHB][hapmap]
rs6787104	0.92[CHB][hapmap]
rs755321	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1009709	chr3:56000827-56294945	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11915970	GLYCTK	cis	cerebellum	SCAN
rs11915970	CCDC66	cis	parietal	SCAN
rs11915970	ERC2	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56157800-56175400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56160000-56170600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:56163000-56171400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:56165200-56170600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:56166400-56170400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:56166400-56171000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:56166400-56173600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:56166600-56170200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:56166600-56170200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:56166600-56171200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:56167400-56170600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:56168200-56170200	Weak transcription	Osteobl	bone
13	chr3:56168200-56171000	Weak transcription	HUVEC	blood vessel
14	chr3:56168200-56171000	Weak transcription	NH-A	brain
15	chr3:56168200-56171600	Weak transcription	Brain Germinal Matrix	brain
16	chr3:56168400-56170000	Weak transcription	A549	lung
17	chr3:56168400-56171200	Weak transcription	HSMMtube	muscle
18	chr3:56168600-56171400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:56168800-56170600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:56168800-56170800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:56168800-56170800	Weak transcription	HSMM	muscle
22	chr3:56168800-56182400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:56169400-56170400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:56169800-56170000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:56169800-56170200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:56169800-56170200	Enhancers	NHEK	skin
27	chr3:56169800-56170400	Enhancers	HMEC	breast

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