Variant report

Variant	rs998788
Chromosome Location	chr5:90318391-90318392
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90315172..90318619-chr5:90676163..90681010,4	MCF-7	breast:
2	chr5:90318099..90320077-chr5:90338969..90341886,2	MCF-7	breast:
3	chr5:90316078..90318522-chr5:90323384..90326123,2	K562	blood:
4	chr5:90312914..90314737-chr5:90316544..90319036,2	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10038122	0.83[CEU][hapmap]
rs10942624	0.88[ASN][1000 genomes]
rs12186662	0.83[ASN][1000 genomes]
rs13179479	0.99[ASN][1000 genomes]
rs13180409	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs1819073	0.95[CHB][hapmap]
rs1819074	0.95[CHB][hapmap]
rs1828177	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1828178	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1848483	0.83[CEU][hapmap]
rs1848485	0.83[CEU][hapmap]
rs1848486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1848487	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1852734	0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1858070	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1976565	0.83[CEU][hapmap]
rs2048217	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2367185	0.83[CEU][hapmap]
rs2367186	0.90[ASN][1000 genomes]
rs2367274	0.88[ASN][1000 genomes]
rs2463775	0.90[ASN][1000 genomes]
rs2662278	0.88[ASN][1000 genomes]
rs2662279	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2662280	0.82[JPT][hapmap]
rs2662281	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2662282	0.99[ASN][1000 genomes]
rs2662283	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2662284	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2697543	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2697544	0.88[ASN][1000 genomes]
rs2697546	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs28875340	0.95[ASN][1000 genomes]
rs4254936	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4454077	0.88[ASN][1000 genomes]
rs4916839	0.84[CEU][hapmap]
rs6452928	0.83[CEU][hapmap]
rs6452930	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6452934	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6865615	0.95[CHB][hapmap]
rs689544	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7706034	0.95[CHB][hapmap]
rs7719311	0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7723511	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7733230	0.95[CHB][hapmap]
rs937920	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[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	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv882369	chr5:90275825-90344149	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90308600-90318400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:90309800-90323200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:90313400-90318400	Weak transcription	A549	lung
4	chr5:90313400-90321600	Weak transcription	Liver	Liver
5	chr5:90313600-90321400	Weak transcription	Small Intestine	intestine
6	chr5:90313800-90320000	Weak transcription	Adipose Nuclei	Adipose
7	chr5:90314000-90319200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:90314200-90319800	Weak transcription	Fetal Stomach	stomach
9	chr5:90314200-90320800	Weak transcription	Fetal Intestine Large	intestine
10	chr5:90314400-90318400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:90314800-90323200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:90314800-90327000	Weak transcription	Gastric	stomach
13	chr5:90315000-90318400	Weak transcription	Fetal Intestine Small	intestine
14	chr5:90315200-90319800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:90315400-90318400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:90316200-90318800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:90316400-90318400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:90316600-90323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:90316800-90318800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:90317000-90323200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:90317000-90325000	Enhancers	Colon Smooth Muscle	Colon
22	chr5:90317400-90318600	Enhancers	Fetal Lung	lung
23	chr5:90317400-90318600	Enhancers	K562	blood
24	chr5:90317400-90318800	Enhancers	Duodenum Mucosa	Duodenum
25	chr5:90317400-90319200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr5:90317600-90324600	Enhancers	Stomach Mucosa	stomach
27	chr5:90317800-90319400	Weak transcription	Psoas Muscle	Psoas
28	chr5:90317800-90323000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:90318000-90318600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:90318000-90318600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr5:90318000-90318800	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr5:90318000-90321800	Enhancers	Rectal Smooth Muscle	rectum
33	chr5:90318200-90318600	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr5:90318200-90318800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr5:90318200-90318800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr5:90318200-90319000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:90318200-90320400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links