Variant report

Variant	rs16825295
Chromosome Location	chr1:186373677-186373678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:186372550..186374489-chr1:186441138..186443259,2	MCF-7	breast:
2	chr1:186373386..186374034-chr1:186451869..186452455,2	MCF-7	breast:
3	chr1:186303450..186305307-chr1:186372043..186373859,2	K562	blood:
4	chr1:186370487..186373941-chr1:186374883..186377860,4	K562	blood:
5	chr1:186373573..186374238-chr1:186954748..186955705,3	K562	blood:
6	chr1:186351329..186353389-chr1:186372131..186374033,2	K562	blood:
7	chr1:186343109..186345591-chr1:186373069..186376266,4	K562	blood:
8	chr1:186373326..186373968-chr1:186954948..186955674,2	MCF-7	breast:
9	chr1:186361659..186366010-chr1:186371455..186375319,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000157181	Chromatin interaction
ENSG00000047410	Chromatin interaction
ENSG00000268662	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10494586	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10911855	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1919198	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2026187	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2037830	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2141393	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2178215	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2383476	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2976253	0.88[ASN][1000 genomes]
rs3115761	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3124814	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3131550	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3131551	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3131558	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766706	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3766709	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs6425026	0.80[ASN][1000 genomes]
rs6657726	0.80[ASN][1000 genomes]
rs6700930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs7756	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.80[ASN][1000 genomes]
rs878041	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8824	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1822818	chr1:186301447-186441585	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats 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	34 gene(s)	inside rSNPs	diseases
6	nsv872589	chr1:186354146-186390303	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	esv1824284	chr1:186358588-186441585	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16825295	C1orf27	cis	cerebellum	SCAN
rs16825295	OCLM	cis	cerebellum	SCAN
rs16825295	OCLM	cis	parietal	SCAN
rs16825295	C1orf27	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186345400-186390600	Weak transcription	Small Intestine	intestine
2	chr1:186345400-186398200	Weak transcription	Spleen	Spleen
3	chr1:186345800-186377400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:186346200-186380400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:186346200-186388400	Weak transcription	Colonic Mucosa	Colon
6	chr1:186346400-186376000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:186346400-186388000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:186346400-186390000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:186348000-186382000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:186348600-186390200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:186355600-186379200	Strong transcription	K562	blood
12	chr1:186355600-186381800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:186360000-186374400	Weak transcription	Fetal Lung	lung
14	chr1:186360000-186379200	Weak transcription	NHLF	lung
15	chr1:186361200-186375000	Weak transcription	HepG2	liver
16	chr1:186361400-186377000	Weak transcription	Fetal Heart	heart
17	chr1:186361600-186388400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:186362400-186405600	Weak transcription	Brain Angular Gyrus	brain
19	chr1:186362800-186375400	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:186362800-186378200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:186362800-186378400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:186362800-186405600	Weak transcription	Right Ventricle	heart
23	chr1:186363000-186378200	Weak transcription	Thymus	Thymus
24	chr1:186363600-186375200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:186364000-186376400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:186364600-186381600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:186365000-186375600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr1:186365400-186390200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:186365600-186374400	Weak transcription	NHEK	skin
30	chr1:186365600-186388000	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:186365600-186395200	Weak transcription	Psoas Muscle	Psoas
32	chr1:186365800-186388000	Weak transcription	Aorta	Aorta
33	chr1:186365800-186388000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:186365800-186388000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:186366200-186393800	Weak transcription	Lung	lung
36	chr1:186366400-186374400	Weak transcription	Fetal Kidney	kidney
37	chr1:186366400-186388000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:186367000-186381000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:186367200-186374400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:186367200-186374400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:186367600-186375200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:186367600-186378400	Weak transcription	Ovary	ovary
43	chr1:186367600-186390000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr1:186367800-186387800	Weak transcription	Fetal Brain Male	brain
45	chr1:186368200-186388000	Weak transcription	Brain Substantia Nigra	brain
46	chr1:186368600-186375400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:186368600-186375800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr1:186368600-186376000	Weak transcription	Fetal Brain Female	brain
49	chr1:186368600-186378000	Weak transcription	Left Ventricle	heart
50	chr1:186368600-186398200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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