Variant report

Variant	rs66475381
Chromosome Location	chr4:90043784-90043785
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:90031396..90034227-chr4:90041663..90045608,5	MCF-7	breast:
2	chr4:90036870..90039187-chr4:90043124..90046686,3	MCF-7	breast:
3	chr4:90036910..90039747-chr4:90043122..90045290,2	MCF-7	breast:
4	chr4:90043352..90045261-chr4:90054968..90057885,2	MCF-7	breast:
5	chr4:90043393..90046238-chr4:90047056..90051826,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TIGD2-4	chr4:90042215-90044000	NONHSAT097383

Variant related genes	Relation type
ENSG00000180346	Chromatin interaction
ENSG00000138640	Chromatin interaction
ENSG00000271359	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10433948	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10433949	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097216	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725475	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11725938	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11726708	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11730277	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12502070	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12507131	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647781	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1533292	0.84[ASN][1000 genomes]
rs1533293	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733448	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4367140	0.85[ASN][1000 genomes]
rs56943497	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58377799	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58633349	0.83[AMR][1000 genomes]
rs59684168	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59799062	0.83[ASN][1000 genomes]
rs60770708	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61138976	0.83[AMR][1000 genomes]
rs61315828	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66500341	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66869930	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67287708	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67412466	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67706608	0.84[ASN][1000 genomes]
rs67850063	0.80[ASN][1000 genomes]
rs6817766	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72613157	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72877639	0.84[ASN][1000 genomes]
rs72877679	0.83[AMR][1000 genomes]
rs72877685	0.83[AMR][1000 genomes]
rs9790655	0.85[ASN][1000 genomes]
rs9994655	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90033400-90048200	Weak transcription	Ovary	ovary
2	chr4:90033400-90049200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:90033600-90043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:90033600-90045600	Weak transcription	Esophagus	oesophagus
5	chr4:90033600-90045600	Weak transcription	Pancreas	Pancrea
6	chr4:90033600-90049200	Weak transcription	Gastric	stomach
7	chr4:90033600-90052200	Weak transcription	Aorta	Aorta
8	chr4:90034000-90044000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:90034200-90044000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:90034400-90044000	Weak transcription	Brain Substantia Nigra	brain
11	chr4:90034800-90049200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:90035400-90044600	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:90035600-90044000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:90036600-90044800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:90037000-90046200	Weak transcription	Primary T cells from cord blood	blood
16	chr4:90039200-90044600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:90039800-90043800	Weak transcription	Liver	Liver
18	chr4:90041400-90043800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:90041600-90044000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:90041600-90044000	Weak transcription	NH-A	brain
21	chr4:90041600-90045200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:90042200-90047600	Enhancers	Fetal Intestine Large	intestine
23	chr4:90042400-90044800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:90042600-90044200	Enhancers	K562	blood
25	chr4:90042600-90049600	Enhancers	Fetal Intestine Small	intestine
26	chr4:90043000-90043800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:90043000-90045200	Enhancers	Stomach Mucosa	stomach
28	chr4:90043200-90043800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:90043200-90043800	Active TSS	A549	lung
30	chr4:90043200-90044400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr4:90043200-90045000	Enhancers	NHEK	skin
32	chr4:90043200-90045800	Enhancers	HMEC	breast
33	chr4:90043400-90044000	Enhancers	Placenta	Placenta
34	chr4:90043400-90050200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:90043600-90044800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:90043600-90044800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:90043600-90045200	Flanking Active TSS	HepG2	liver
38	chr4:90043600-90046000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr4:90043600-90046000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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