Variant report

Variant	rs3899794
Chromosome Location	chr4:15164829-15164830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:15003502..15006287-chr4:15164170..15165943,2	MCF-7	breast:
2	chr4:15151866..15154106-chr4:15163665..15166328,2	K562	blood:
3	chr4:15044990..15045540-chr4:15164442..15165368,4	MCF-7	breast:
4	chr4:15037859..15038669-chr4:15164398..15164952,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247624	Chromatin interaction
ENSG00000137449	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12646654	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12647022	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12647052	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12651481	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1378338	0.80[CHD][hapmap]
rs1455202	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1455204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16891494	0.82[ASN][1000 genomes]
rs16891498	0.82[ASN][1000 genomes]
rs16891503	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1813151	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28530620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57804406	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449105	0.88[YRI][hapmap]
rs930830	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3899794	SNORD27	trans	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15161000-15166200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:15162200-15165000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr4:15162400-15165200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr4:15162600-15165000	Enhancers	H9 Cell Line	embryonic stem cell
5	chr4:15162600-15165200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr4:15163400-15166200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:15163600-15165200	Enhancers	Brain Substantia Nigra	brain
8	chr4:15163600-15166000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:15163600-15171200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:15163800-15165200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr4:15163800-15166000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr4:15164000-15166000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:15164000-15166200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:15164000-15187800	Weak transcription	Aorta	Aorta
15	chr4:15164200-15165000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr4:15164400-15165400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:15164400-15166000	Weak transcription	Hela-S3	cervix
18	chr4:15164400-15166200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:15164600-15165000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:15164600-15165200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr4:15164600-15165400	Enhancers	K562	blood
22	chr4:15164800-15165000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:15164800-15165400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:15164800-15165400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
25	chr4:15164800-15166200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:15164800-15166400	Weak transcription	Osteobl	bone

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