Variant report

Variant	rs934278
Chromosome Location	chr2:56070352-56070353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:56070321..56072197-chr2:56112589..56114898,2	MCF-7	breast:
2	chr2:56004031..56006518-chr2:56068498..56070427,2	MCF-7	breast:
3	chr2:56068913..56070987-chr2:56145608..56147872,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11125607	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11125608	0.89[ASN][1000 genomes]
rs12478566	0.86[ASN][1000 genomes]
rs1344732	0.85[ASN][1000 genomes]
rs1346781	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1346783	0.89[ASN][1000 genomes]
rs1346787	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1346790	0.93[ASN][1000 genomes]
rs1367225	0.85[ASN][1000 genomes]
rs1367226	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1367228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1430189	0.88[ASN][1000 genomes]
rs1430190	0.85[ASN][1000 genomes]
rs1430191	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs1430203	0.93[ASN][1000 genomes]
rs1897114	0.96[ASN][1000 genomes]
rs1960050	0.95[ASN][1000 genomes]
rs1985160	0.85[ASN][1000 genomes]
rs1985162	0.85[ASN][1000 genomes]
rs2052933	0.88[ASN][1000 genomes]
rs2115876	0.93[ASN][1000 genomes]
rs2115878	0.89[ASN][1000 genomes]
rs3791676	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4352264	0.95[ASN][1000 genomes]
rs4672074	0.89[ASN][1000 genomes]
rs4672075	0.83[ASN][1000 genomes]
rs6545523	0.86[ASN][1000 genomes]
rs6545526	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545527	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6708796	0.93[ASN][1000 genomes]
rs6712017	0.88[ASN][1000 genomes]
rs6714513	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs6733730	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6743114	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6749785	0.86[ASN][1000 genomes]
rs6751403	0.95[ASN][1000 genomes]
rs6753814	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs6757057	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7426380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7572523	0.93[ASN][1000 genomes]
rs7574127	0.81[ASN][1000 genomes]
rs7607070	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7609520	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs934278	CCDC85A	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56066800-56070600	Weak transcription	Liver	Liver
2	chr2:56066800-56082600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:56068600-56071400	Flanking Active TSS	A549	lung
4	chr2:56068600-56071800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:56068800-56070400	Enhancers	Placenta	Placenta
6	chr2:56068800-56071000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:56068800-56071200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:56068800-56071400	Enhancers	Fetal Intestine Small	intestine
9	chr2:56068800-56072000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:56068800-56072000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:56068800-56072000	Enhancers	Osteobl	bone
12	chr2:56069000-56071000	Enhancers	HepG2	liver
13	chr2:56069000-56071200	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr2:56069000-56071400	Enhancers	Fetal Intestine Large	intestine
15	chr2:56069000-56071600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:56069000-56071600	Enhancers	NHDF-Ad	bronchial
17	chr2:56069000-56071600	Enhancers	NHLF	lung
18	chr2:56069000-56072200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:56069200-56071400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr2:56069200-56071400	Enhancers	HSMM	muscle
21	chr2:56069200-56071600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:56069200-56071600	Enhancers	NHEK	skin
23	chr2:56069200-56071800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:56069400-56070600	Weak transcription	Adipose Nuclei	Adipose
25	chr2:56069600-56070800	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr2:56069800-56071000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:56069800-56071400	Enhancers	Fetal Lung	lung
28	chr2:56069800-56071400	Enhancers	NH-A	brain
29	chr2:56070000-56070400	Flanking Active TSS	Stomach Mucosa	stomach
30	chr2:56070000-56070600	Enhancers	Pancreas	Pancrea
31	chr2:56070000-56070800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr2:56070000-56071000	Enhancers	Fetal Kidney	kidney
33	chr2:56070000-56071200	Enhancers	HSMMtube	muscle
34	chr2:56070200-56070400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:56070200-56070400	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr2:56070200-56070400	Enhancers	Gastric	stomach
37	chr2:56070200-56070600	Enhancers	Esophagus	oesophagus
38	chr2:56070200-56070600	Enhancers	Ovary	ovary
39	chr2:56070200-56070600	Enhancers	HUVEC	blood vessel
40	chr2:56070200-56070800	Enhancers	Small Intestine	intestine
41	chr2:56070200-56070800	Enhancers	K562	blood
42	chr2:56070200-56071200	Flanking Active TSS	Hela-S3	cervix
43	chr2:56070200-56071400	Enhancers	HMEC	breast
44	chr2:56070200-56073000	Enhancers	Primary monocytes fromperipheralblood	blood

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