Variant report

Variant	rs1666263
Chromosome Location	chr17:38630080-38630081
allele	C/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:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38604588..38605147-chr17:38629467..38630083,2	MCF-7	breast:
2	chr17:38627597..38631126-chr17:38634804..38638416,4	K562	blood:
3	chr17:38629230..38633367-chr17:38687189..38689523,3	MCF-7	breast:
4	chr17:38604253..38605191-chr17:38629557..38630478,2	MCF-7	breast:
5	chr17:38617634..38619166-chr17:38628984..38631978,2	MCF-7	breast:
6	chr17:38603659..38605432-chr17:38628580..38630648,2	MCF-7	breast:
7	chr17:38629814..38633387-chr17:38676751..38679736,4	MCF-7	breast:
8	chr17:38604253..38605216-chr17:38629557..38630486,3	MCF-7	breast:
9	chr17:38600754..38602507-chr17:38629659..38632634,3	K562	blood:
10	chr17:38598950..38601865-chr17:38628888..38632301,4	MCF-7	breast:
11	chr17:38598427..38603183-chr17:38627636..38631159,5	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNS4-2	chr17:38629806-38631541	NONHSAT053550

No data

Variant related genes	Relation type
ENSG00000131746	Chromatin interaction
ENSG00000141753	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11078948	0.86[ASN][1000 genomes]
rs11652694	0.97[ASN][1000 genomes]
rs11654599	0.81[ASN][1000 genomes]
rs17557153	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2122614	0.91[ASN][1000 genomes]
rs475087	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56308624	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs627857	0.89[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7211995	0.96[ASN][1000 genomes]
rs7224214	0.81[ASN][1000 genomes]
rs8079359	0.89[CHB][hapmap]
rs9303288	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9893209	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1058185	chr17:38629339-38689908	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38619200-38632000	Weak transcription	Right Atrium	heart
2	chr17:38620600-38632200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr17:38626600-38631600	Enhancers	Fetal Stomach	stomach
4	chr17:38627000-38633000	Enhancers	Rectal Smooth Muscle	rectum
5	chr17:38627200-38631800	Enhancers	Placenta	Placenta
6	chr17:38627200-38631800	Enhancers	Hela-S3	cervix
7	chr17:38627200-38632000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr17:38627200-38632400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr17:38627200-38633000	Enhancers	Colon Smooth Muscle	Colon
10	chr17:38627200-38633400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr17:38627200-38633400	Enhancers	Ovary	ovary
12	chr17:38627400-38633200	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr17:38627400-38646200	Weak transcription	Gastric	stomach
14	chr17:38627600-38630800	Weak transcription	Spleen	Spleen
15	chr17:38627600-38632800	Enhancers	Liver	Liver
16	chr17:38627800-38630800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr17:38627800-38630800	Enhancers	A549	lung
18	chr17:38627800-38631000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr17:38627800-38631400	Weak transcription	Fetal Lung	lung
20	chr17:38628000-38630400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr17:38628000-38630600	Weak transcription	K562	blood
22	chr17:38628200-38630600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr17:38628400-38630200	Enhancers	Esophagus	oesophagus
24	chr17:38628400-38630600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr17:38628400-38631000	Weak transcription	Fetal Intestine Small	intestine
26	chr17:38628600-38630800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr17:38628600-38632800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:38628800-38631800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr17:38628800-38632000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr17:38628800-38632200	Weak transcription	NH-A	brain
31	chr17:38628800-38636400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr17:38629000-38630800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr17:38629000-38631800	Weak transcription	NHLF	lung
34	chr17:38629000-38631800	Weak transcription	Osteobl	bone
35	chr17:38629000-38632000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr17:38629200-38632800	Enhancers	Stomach Mucosa	stomach
37	chr17:38629400-38630200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr17:38629400-38632000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr17:38629400-38632000	Weak transcription	NHDF-Ad	bronchial
40	chr17:38629600-38630200	Enhancers	Duodenum Mucosa	Duodenum
41	chr17:38629800-38632400	Enhancers	Fetal Intestine Large	intestine
42	chr17:38629800-38632800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr17:38629800-38632800	Weak transcription	NHEK	skin
44	chr17:38629800-38633000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr17:38630000-38630200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr17:38630000-38630600	Enhancers	Stomach Smooth Muscle	stomach
47	chr17:38630000-38630800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr17:38630000-38631800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr17:38630000-38631800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr17:38630000-38631800	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links