Variant report

Variant	rs6892128
Chromosome Location	chr5:60571376-60571377
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60457988..60459859-chr5:60568864..60572383,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188725	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10037643	0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10052765	0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10062338	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10065444	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10071763	0.95[ASN][1000 genomes]
rs10434526	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10461467	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10471510	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10939888	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939890	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939892	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10939893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12189426	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12518152	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12523278	0.84[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs12696979	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12696980	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13175564	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs34439016	0.99[ASN][1000 genomes]
rs35310874	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4129437	0.81[ASN][1000 genomes]
rs4315878	1.00[MEX][hapmap]
rs4400074	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4441832	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4540126	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4640746	1.00[MEX][hapmap]
rs4699974	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4699975	0.93[ASN][1000 genomes]
rs6864367	0.93[ASN][1000 genomes]
rs6867268	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6867417	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6885499	0.93[ASN][1000 genomes]
rs7448844	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7737448	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9291718	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

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	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription 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	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6892128	DEPDC1B	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60550400-60573400	Weak transcription	Gastric	stomach
2	chr5:60561000-60573200	Weak transcription	Brain Hippocampus Middle	brain
3	chr5:60564600-60575400	Weak transcription	Fetal Intestine Small	intestine
4	chr5:60564600-60576000	Weak transcription	Psoas Muscle	Psoas
5	chr5:60566000-60573200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:60566400-60573000	Weak transcription	Stomach Mucosa	stomach
7	chr5:60566600-60573800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr5:60567800-60577200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr5:60568200-60573000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:60568800-60573200	Weak transcription	HSMMtube	muscle
11	chr5:60569000-60571800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:60569000-60572800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:60569000-60572800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr5:60569000-60574000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr5:60569200-60574600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr5:60569400-60571600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:60569400-60573000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:60569400-60573000	Weak transcription	Brain Substantia Nigra	brain
19	chr5:60569400-60573200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:60569400-60574000	Enhancers	Primary B cells from cord blood	blood
21	chr5:60569600-60572800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:60569800-60572200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:60569800-60573200	Weak transcription	Right Atrium	heart
24	chr5:60570000-60572000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:60570000-60573200	Enhancers	Muscle Satellite Cultured Cells	--
26	chr5:60570000-60573800	Enhancers	NHLF	lung
27	chr5:60570200-60572000	Enhancers	HSMM	muscle
28	chr5:60570200-60573200	Enhancers	NHDF-Ad	bronchial
29	chr5:60570400-60572000	Enhancers	Fetal Lung	lung
30	chr5:60570600-60571600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:60570600-60573200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:60570600-60573200	Enhancers	HUVEC	blood vessel
33	chr5:60570800-60571800	Enhancers	Adipose Nuclei	Adipose
34	chr5:60570800-60573200	Weak transcription	Colon Smooth Muscle	Colon
35	chr5:60570800-60573600	Enhancers	Primary hematopoietic stem cells	blood
36	chr5:60570800-60573800	Enhancers	A549	lung
37	chr5:60570800-60574400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:60571000-60571400	Enhancers	Ovary	ovary
39	chr5:60571000-60571600	Enhancers	Small Intestine	intestine
40	chr5:60571000-60572000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:60571000-60572000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:60571000-60572000	Enhancers	Lung	lung
43	chr5:60571000-60572000	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr5:60571000-60572000	Enhancers	Spleen	Spleen
45	chr5:60571000-60572400	Enhancers	GM12878-XiMat	blood
46	chr5:60571000-60572800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr5:60571000-60573400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:60571000-60573400	Enhancers	Placenta	Placenta
49	chr5:60571000-60573600	Enhancers	Primary B cells from peripheral blood	blood
50	chr5:60571000-60573800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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