Variant report

Variant	rs4077408
Chromosome Location	chr1:210760444-210760445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11119543	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119544	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119550	0.81[ASN][1000 genomes]
rs12024921	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12034711	0.89[EUR][1000 genomes]
rs12069347	0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs12745924	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4951722	0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs6691952	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv873149	chr1:210749312-210793972	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4077408	NUCKS1	cis	cerebellum	SCAN
rs4077408	RASSF5	cis	cerebellum	SCAN
rs4077408	IKBKE	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210752200-210761200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:210756200-210761000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:210756200-210771800	Weak transcription	Left Ventricle	heart
4	chr1:210757200-210761200	Weak transcription	HSMM	muscle
5	chr1:210758200-210761000	Weak transcription	Gastric	stomach
6	chr1:210758400-210761000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:210758400-210761000	Weak transcription	Osteobl	bone
8	chr1:210758600-210763000	Weak transcription	A549	lung
9	chr1:210759200-210760800	Enhancers	Brain Cingulate Gyrus	brain
10	chr1:210759400-210761400	Enhancers	Fetal Brain Male	brain
11	chr1:210759600-210760600	Enhancers	Brain Angular Gyrus	brain
12	chr1:210759600-210761000	Enhancers	Brain Hippocampus Middle	brain
13	chr1:210759600-210761000	Enhancers	Brain Substantia Nigra	brain
14	chr1:210759600-210761200	Enhancers	Colon Smooth Muscle	Colon
15	chr1:210759800-210761000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:210759800-210761200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:210760000-210761200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:210760000-210761400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:210760000-210761600	Enhancers	HSMMtube	muscle
20	chr1:210760200-210760600	Weak transcription	Fetal Heart	heart
21	chr1:210760200-210761400	Enhancers	Fetal Muscle Leg	muscle
22	chr1:210760200-210761600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:210760400-210763200	Weak transcription	Brain Anterior Caudate	brain
24	chr1:210760400-210763200	Weak transcription	Brain Inferior Temporal Lobe	brain

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