Variant report

Variant	rs4282879
Chromosome Location	chr1:210801563-210801564
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12116836	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap]
rs12122067	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs12133319	0.82[ASW][hapmap];0.81[CHB][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.87[AFR][1000 genomes]
rs3935665	0.89[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs7349100	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap]
rs7533989	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7547973	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv522480	chr1:210779936-210848344	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases
3	esv1825229	chr1:210789477-210854976	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4282879	KCNH1	cis	cerebellum	SCAN
rs4282879	C1orf107	cis	cerebellum	SCAN
rs4282879	LPGAT1	cis	parietal	SCAN
rs4282879	C1orf97	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210790400-210801800	Weak transcription	Pancreas	Pancrea
2	chr1:210790600-210807000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:210795400-210822600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:210795800-210806600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:210797000-210801800	Weak transcription	Ovary	ovary
6	chr1:210798600-210806200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:210799000-210804600	Weak transcription	Brain Angular Gyrus	brain
8	chr1:210799000-210804600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:210799200-210801600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:210799200-210805000	Weak transcription	Brain Anterior Caudate	brain
11	chr1:210799200-210807000	Weak transcription	HSMM	muscle
12	chr1:210799400-210802600	Weak transcription	Brain Substantia Nigra	brain
13	chr1:210799800-210801600	Weak transcription	HSMMtube	muscle
14	chr1:210800200-210802000	Enhancers	Right Ventricle	heart
15	chr1:210800800-210802000	Enhancers	Colon Smooth Muscle	Colon
16	chr1:210800800-210802000	Enhancers	A549	lung
17	chr1:210801000-210806600	Weak transcription	Right Atrium	heart
18	chr1:210801200-210801600	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr1:210801200-210802000	Enhancers	Brain Hippocampus Middle	brain
20	chr1:210801400-210801600	Enhancers	Aorta	Aorta
21	chr1:210801400-210801800	Enhancers	Left Ventricle	heart
22	chr1:210801400-210801800	Enhancers	Rectal Smooth Muscle	rectum
23	chr1:210801400-210802000	Enhancers	Brain Inferior Temporal Lobe	brain

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