Variant report

Variant	rs4915606
Chromosome Location	chr1:62761852-62761853
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62759279..62761889-chr1:62763662..62766108,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201153	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10157938	0.83[ASN][1000 genomes]
rs10465842	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493318	0.90[JPT][hapmap]
rs10889318	0.90[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11207955	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs11207956	0.90[JPT][hapmap]
rs12031176	0.86[JPT][hapmap]
rs12038843	0.90[JPT][hapmap]
rs12127630	0.81[JPT][hapmap]
rs12138544	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12749514	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1325740	0.89[ASN][1000 genomes]
rs1886833	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1886834	0.90[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1925827	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366207	0.98[ASN][1000 genomes]
rs2477874	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666509	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2765266	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765268	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765269	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35126231	0.98[ASN][1000 genomes]
rs3850629	0.82[JPT][hapmap]
rs3861936	0.89[JPT][hapmap]
rs4915607	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587966	0.87[ASN][1000 genomes]
rs6658312	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675508	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6675627	0.89[ASN][1000 genomes]
rs7514266	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881548	0.80[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs9803815	0.90[JPT][hapmap]

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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	nsv431712	chr1:62759369-62766001	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4915606	DNAJC6	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62754400-62773400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:62754800-62765200	Weak transcription	Fetal Heart	heart
3	chr1:62756200-62765000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:62756400-62764800	Weak transcription	HepG2	liver
5	chr1:62759800-62765400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:62759800-62770800	Enhancers	Fetal Muscle Leg	muscle
7	chr1:62760000-62762400	Enhancers	H1 Cell Line	embryonic stem cell
8	chr1:62760400-62762000	Enhancers	Brain Angular Gyrus	brain
9	chr1:62760400-62762400	Enhancers	Primary T cells from cord blood	blood
10	chr1:62760400-62762400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr1:62760800-62762400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:62761000-62762000	Enhancers	H9 Cell Line	embryonic stem cell
13	chr1:62761000-62762000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:62761000-62762200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr1:62761000-62762200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:62761000-62762200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:62761000-62762400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:62761000-62762400	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr1:62761000-62762400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:62761000-62763200	Enhancers	Fetal Stomach	stomach
21	chr1:62761200-62762000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:62761200-62762000	Enhancers	Colonic Mucosa	Colon
23	chr1:62761200-62762000	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr1:62761200-62762200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:62761200-62762200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr1:62761200-62762200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr1:62761200-62762200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr1:62761200-62762200	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr1:62761200-62762200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:62761200-62762200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:62761200-62762200	Enhancers	Fetal Lung	lung
32	chr1:62761200-62762200	Enhancers	Placenta	Placenta
33	chr1:62761200-62762200	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr1:62761200-62762200	Enhancers	HSMMtube	muscle
35	chr1:62761200-62762200	Enhancers	NH-A	brain
36	chr1:62761200-62762200	Enhancers	NHDF-Ad	bronchial
37	chr1:62761200-62762200	Enhancers	NHEK	skin
38	chr1:62761200-62762400	Enhancers	Primary hematopoietic stem cells	blood
39	chr1:62761200-62762400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
40	chr1:62761200-62762400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:62761200-62762400	Enhancers	Brain Anterior Caudate	brain
42	chr1:62761200-62762400	Enhancers	Brain Germinal Matrix	brain
43	chr1:62761200-62762600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:62761200-62763200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:62761400-62762000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr1:62761400-62762000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr1:62761400-62762200	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr1:62761400-62762200	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr1:62761400-62762200	Enhancers	Fetal Thymus	thymus
50	chr1:62761400-62762200	Enhancers	GM12878-XiMat	blood

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