Variant report

Variant	rs1378800
Chromosome Location	chr3:157181148-157181149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:157175083..157179044-chr3:157180593..157185169,5	K562	blood:
2	chr3:157176898..157178471-chr3:157180465..157182221,2	K562	blood:
3	chr3:157181063..157183847-chr3:157192329..157195122,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1009873	0.96[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11709669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1456100	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1456101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1456102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16827662	0.86[YRI][hapmap]
rs17391399	0.87[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17470517	0.82[CHB][hapmap]
rs1824056	0.82[CHB][hapmap]
rs1838143	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4679795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680370	0.82[CHB][hapmap]
rs6794511	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9815250	0.82[CHB][hapmap]
rs9841781	0.82[CHB][hapmap]
rs9859018	0.82[CHB][hapmap]
rs9873474	0.82[CHB][hapmap]
rs9877620	0.82[CHB][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	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1378800	C3orf55	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157160400-157195000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:157161200-157186600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:157164600-157185400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:157170200-157187000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:157175400-157181200	Weak transcription	Lung	lung
6	chr3:157178600-157182000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:157178800-157181400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:157178800-157181400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:157178800-157181600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:157178800-157181800	Weak transcription	HSMMtube	muscle
11	chr3:157178800-157181800	Weak transcription	NH-A	brain
12	chr3:157178800-157182000	Weak transcription	Fetal Stomach	stomach
13	chr3:157179400-157181200	Weak transcription	NHLF	lung
14	chr3:157179400-157181600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:157179400-157184800	Weak transcription	HSMM	muscle
16	chr3:157180200-157181200	Strong transcription	Osteobl	bone
17	chr3:157180200-157186000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:157180400-157181400	Weak transcription	HUVEC	blood vessel
19	chr3:157180400-157185400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:157180800-157186000	Enhancers	NHDF-Ad	bronchial
21	chr3:157181000-157186400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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