Variant report

Variant	rs1534154
Chromosome Location	chr3:119311030-119311031
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119305600..119307239-chr3:119310554..119312770,2	K562	blood:
2	chr3:119309459..119312426-chr3:119393975..119396413,2	MCF-7	breast:
3	chr3:119305600..119307838-chr3:119310497..119312054,2	K562	blood:
4	chr11:93474164..93475004-chr3:119310794..119311294,2	NB4	blood:
5	chr3:119310790..119313134-chr3:119314484..119316186,2	K562	blood:
6	chr3:119309806..119311897-chr3:119315565..119318074,3	K562	blood:

Variant related genes	Relation type
ENSG00000144837	Chromatin interaction
ENSG00000182919	Chromatin interaction
ENSG00000166012	Chromatin interaction
ENSG00000138495	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10433338	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1525838	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1723969	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.94[ASN][1000 genomes]
rs1797831	0.94[ASN][1000 genomes]
rs1797832	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2049501	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2171025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248483	0.94[ASN][1000 genomes]
rs2251566	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2272267	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272268	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272269	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272270	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2629399	0.94[ASN][1000 genomes]
rs2629400	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2629408	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2670293	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2670298	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2688637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2688638	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2688639	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2688646	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688647	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688648	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2692612	0.94[ASN][1000 genomes]
rs2692613	0.92[ASN][1000 genomes]
rs2692614	0.94[ASN][1000 genomes]
rs2692615	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2692621	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692623	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474926	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs485257	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs487124	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs528765	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530389	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs530783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536624	0.95[CHB][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs538136	0.99[ASN][1000 genomes]
rs551885	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555525	0.98[ASN][1000 genomes]
rs55670246	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55801535	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56197198	0.83[EUR][1000 genomes]
rs58020513	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs593968	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs666134	1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs6807201	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[TSI][hapmap];0.94[ASN][1000 genomes]
rs6807613	0.92[ASN][1000 genomes]
rs72954966	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv3963	chr3:119301064-119345904	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1534154	CCDC85A	trans	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119299200-119314600	Weak transcription	Ovary	ovary
2	chr3:119299200-119315000	Weak transcription	Gastric	stomach
3	chr3:119299400-119314200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:119299400-119314400	Weak transcription	Brain Angular Gyrus	brain
5	chr3:119299600-119314200	Weak transcription	Brain Substantia Nigra	brain
6	chr3:119299600-119314200	Weak transcription	Psoas Muscle	Psoas
7	chr3:119299800-119314600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:119299800-119314600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:119299800-119318000	Weak transcription	Fetal Heart	heart
10	chr3:119305400-119314400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:119305600-119314200	Weak transcription	Lung	lung
12	chr3:119305600-119314200	Weak transcription	HSMMtube	muscle
13	chr3:119305800-119314600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:119306000-119316800	Weak transcription	Pancreas	Pancrea
15	chr3:119306600-119314200	Weak transcription	Right Ventricle	heart
16	chr3:119307400-119311200	Weak transcription	Placenta	Placenta
17	chr3:119307400-119314200	Weak transcription	Right Atrium	heart
18	chr3:119307600-119316400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:119307800-119314400	Weak transcription	Adipose Nuclei	Adipose
20	chr3:119308200-119314000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:119308200-119314200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:119308200-119314800	Weak transcription	Aorta	Aorta
23	chr3:119308400-119314200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:119308400-119314200	Weak transcription	Left Ventricle	heart
25	chr3:119308600-119314600	Weak transcription	Osteobl	bone
26	chr3:119308800-119311400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:119309000-119311600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:119309800-119314800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:119310000-119314600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:119310600-119319800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:119311000-119311200	Enhancers	Fetal Lung	lung
32	chr3:119311000-119311400	Weak transcription	GM12878-XiMat	blood
33	chr3:119311000-119315000	Weak transcription	Spleen	Spleen
34	chr3:119311000-119317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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