Variant report

Variant	rs9899955
Chromosome Location	chr17:38176476-38176477
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38174242..38176838-chr17:38278779..38280861,2	MCF-7	breast:
2	chr17:38175295..38180645-chr17:38181007..38185256,8	MCF-7	breast:
3	chr17:38135295..38137617-chr17:38176453..38178456,2	K562	blood:
4	chr17:38174715..38177590-chr17:38209751..38212777,3	K562	blood:
5	chr17:38175071..38177613-chr17:38178105..38180812,3	MCF-7	breast:
6	chr17:38174842..38178903-chr17:38208625..38211251,3	K562	blood:
7	chr17:38172859..38176802-chr17:38178682..38181500,4	K562	blood:
8	chr17:38141745..38144493-chr17:38173834..38176591,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108344	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000188895	Chromatin interaction
ENSG00000238793	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1042657	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12938879	0.88[EUR][1000 genomes]
rs2071369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071370	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2302775	0.95[ASN][1000 genomes]
rs2302778	0.95[ASN][1000 genomes]
rs3826330	0.88[EUR][1000 genomes]
rs3859190	0.86[EUR][1000 genomes]
rs3916061	0.83[EUR][1000 genomes]
rs3934886	0.82[ASN][1000 genomes]
rs4795411	0.88[EUR][1000 genomes]
rs4795417	0.88[EUR][1000 genomes]
rs4795421	0.91[EUR][1000 genomes]
rs6503532	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6503534	0.82[ASN][1000 genomes]
rs7503939	0.95[ASN][1000 genomes]
rs8068253	0.91[EUR][1000 genomes]
rs8070452	0.81[ASN][1000 genomes]
rs9748108	0.95[EUR][1000 genomes]
rs9900199	0.82[EUR][1000 genomes]
rs9903987	0.88[EUR][1000 genomes]
rs9913632	0.92[EUR][1000 genomes];1.00[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	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38166800-38177400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr17:38166800-38178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:38170000-38178800	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr17:38170400-38177600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr17:38170400-38181600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr17:38171400-38186000	Weak transcription	Small Intestine	intestine
8	chr17:38171600-38176800	Weak transcription	Hela-S3	cervix
9	chr17:38172400-38178400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr17:38172800-38176800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr17:38173000-38176600	Genic enhancers	Fetal Stomach	stomach
12	chr17:38173000-38179600	Strong transcription	Fetal Intestine Small	intestine
13	chr17:38173000-38181400	Weak transcription	Fetal Kidney	kidney
14	chr17:38173200-38176800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr17:38173400-38183800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:38173400-38192800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr17:38173600-38176600	Enhancers	Psoas Muscle	Psoas
18	chr17:38173600-38180200	Genic enhancers	Fetal Muscle Trunk	muscle
19	chr17:38173600-38180400	Genic enhancers	NHLF	lung
20	chr17:38173600-38182000	Strong transcription	Thymus	Thymus
21	chr17:38173800-38176800	Enhancers	Stomach Mucosa	stomach
22	chr17:38173800-38179400	Strong transcription	Fetal Intestine Large	intestine
23	chr17:38173800-38179800	Genic enhancers	Spleen	Spleen
24	chr17:38173800-38180600	Strong transcription	Brain Anterior Caudate	brain
25	chr17:38173800-38181400	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr17:38173800-38181800	Strong transcription	Primary T cells from cord blood	blood
27	chr17:38173800-38182400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr17:38174000-38176600	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr17:38174000-38178200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr17:38174000-38192600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr17:38174000-38193800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr17:38174200-38176600	Genic enhancers	Lung	lung
33	chr17:38174200-38179600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr17:38174200-38180400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr17:38174200-38180800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr17:38174200-38183200	Strong transcription	Placenta	Placenta
37	chr17:38174200-38183400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr17:38174200-38183400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr17:38174200-38187400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:38174400-38176600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr17:38174400-38179200	Strong transcription	Pancreas	Pancrea
42	chr17:38174400-38179800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr17:38174400-38183200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr17:38174400-38193200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr17:38174600-38177200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr17:38174600-38177400	Genic enhancers	NHEK	skin
47	chr17:38174600-38178000	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr17:38174600-38180400	Genic enhancers	Fetal Muscle Leg	muscle
49	chr17:38174600-38181400	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr17:38174600-38181800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links