Variant report

Variant	rs3909688
Chromosome Location	chr18:13505299-13505300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13504939..13506992-chr18:13515304..13518121,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13381731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1648592	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1648601	0.81[ASN][1000 genomes]
rs2567168	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2847114	0.82[ASN][1000 genomes]
rs8090616	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8090627	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs890472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs890473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs890474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9965287	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[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	nsv531246	chr18:13298774-14082028	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13471000-13537400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr18:13499200-13505800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr18:13499400-13505400	Genic enhancers	Fetal Thymus	thymus
4	chr18:13499400-13506000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr18:13499600-13506000	Weak transcription	Primary B cells from cord blood	blood
6	chr18:13499600-13539200	Weak transcription	Gastric	stomach
7	chr18:13499800-13514200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr18:13499800-13531000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr18:13500000-13516800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr18:13500400-13517400	Weak transcription	Spleen	Spleen
11	chr18:13501400-13505600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr18:13501400-13505800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr18:13501400-13518200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr18:13501600-13505800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr18:13501600-13505800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr18:13501600-13525000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr18:13501800-13530600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr18:13502200-13505400	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr18:13502600-13507000	Genic enhancers	Thymus	Thymus
20	chr18:13502800-13525200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr18:13503000-13517000	Weak transcription	Adipose Nuclei	Adipose
22	chr18:13503000-13519200	Weak transcription	Pancreas	Pancrea
23	chr18:13503200-13505800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr18:13503200-13506000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr18:13503200-13506600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr18:13503200-13508000	Weak transcription	Fetal Stomach	stomach
27	chr18:13503200-13511800	Weak transcription	Brain Anterior Caudate	brain
28	chr18:13503200-13514600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr18:13503200-13517200	Weak transcription	Fetal Lung	lung
30	chr18:13503200-13521000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr18:13503400-13505800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr18:13503400-13505800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr18:13503400-13506000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr18:13503400-13511600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr18:13503400-13512200	Weak transcription	Liver	Liver
36	chr18:13503400-13517400	Weak transcription	Aorta	Aorta
37	chr18:13503600-13505800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr18:13503800-13508200	Weak transcription	Fetal Brain Female	brain
39	chr18:13503800-13512800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr18:13504200-13509000	Weak transcription	Left Ventricle	heart
41	chr18:13504400-13505800	Weak transcription	Colonic Mucosa	Colon
42	chr18:13504800-13505600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr18:13504800-13506400	Enhancers	Primary T cells fromperipheralblood	blood
44	chr18:13505000-13506000	Weak transcription	Fetal Muscle Leg	muscle
45	chr18:13505000-13508200	Weak transcription	Psoas Muscle	Psoas
46	chr18:13505000-13509000	Weak transcription	Right Atrium	heart
47	chr18:13505000-13536000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr18:13505200-13506600	Weak transcription	Fetal Heart	heart
49	chr18:13505200-13506800	Enhancers	Primary T cells from cord blood	blood
50	chr18:13505200-13507600	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links