Variant report

Variant	rs28093
Chromosome Location	chr5:96052050-96052051
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96038517..96040700-chr5:96049207..96053168,5	K562	blood:
2	chr5:96050817..96052390-chr5:96054162..96057341,3	K562	blood:
3	chr5:96049970..96053832-chr5:96077718..96080469,3	K562	blood:
4	chr5:96050730..96052742-chr5:96268352..96271108,2	K562	blood:
5	chr5:96038517..96042326-chr5:96049258..96052304,3	K562	blood:

Variant related genes	Relation type
ENSG00000249180	Chromatin interaction
ENSG00000153113	Chromatin interaction
ENSG00000113441	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10067766	0.85[JPT][hapmap]
rs1421911	0.86[JPT][hapmap]
rs151835	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs151904	0.86[JPT][hapmap]
rs152005	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs152014	0.86[JPT][hapmap]
rs152017	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs152020	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs2351245	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs26482	0.86[JPT][hapmap]
rs26483	0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs26484	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs26485	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs26503	0.86[JPT][hapmap]
rs26504	0.86[JPT][hapmap]
rs28104	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs31248	0.86[JPT][hapmap]
rs31249	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs31250	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4590196	0.86[JPT][hapmap]
rs6556937	0.86[JPT][hapmap]
rs6860934	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6897588	0.86[JPT][hapmap]
rs7704167	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs7705824	0.86[JPT][hapmap]
rs7733671	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv830411	chr5:96045168-96187817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28093	CAST	cis	parietal	SCAN
rs28093	CAST	cis	lymphoblastoid	seeQTL
rs28093	CAST	cis	cerebellum	SCAN
rs28093	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs28093	CAST	cis	Whole Blood	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96039200-96054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:96039200-96054400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:96039200-96054400	Weak transcription	Spleen	Spleen
4	chr5:96039200-96059800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:96039600-96063600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr5:96040000-96054400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:96040000-96054400	Weak transcription	Fetal Stomach	stomach
8	chr5:96041600-96054600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr5:96042800-96076200	Weak transcription	GM12878-XiMat	blood
10	chr5:96043600-96054400	Weak transcription	Esophagus	oesophagus
11	chr5:96045000-96052200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr5:96045800-96056800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:96047400-96054800	Enhancers	Fetal Heart	heart
14	chr5:96047800-96055000	Enhancers	Fetal Intestine Large	intestine
15	chr5:96048000-96054400	Weak transcription	Brain Angular Gyrus	brain
16	chr5:96048400-96052600	Weak transcription	Pancreas	Pancrea
17	chr5:96048400-96054400	Weak transcription	Lung	lung
18	chr5:96048600-96054800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr5:96049000-96054800	Enhancers	Stomach Mucosa	stomach
20	chr5:96049200-96054400	Enhancers	Fetal Intestine Small	intestine
21	chr5:96049600-96052400	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr5:96049600-96053400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:96049600-96053400	Enhancers	Liver	Liver
24	chr5:96049600-96054800	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr5:96049800-96052200	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr5:96049800-96052200	Enhancers	Right Ventricle	heart
27	chr5:96049800-96052600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr5:96049800-96054800	Enhancers	K562	blood
29	chr5:96049800-96058400	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr5:96050000-96052400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:96050200-96053400	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr5:96050200-96053600	Enhancers	Small Intestine	intestine
33	chr5:96050200-96053800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr5:96050400-96052400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:96050400-96053200	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr5:96050400-96053800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:96050800-96052200	Strong transcription	Primary B cells from peripheral blood	blood
38	chr5:96050800-96053000	Weak transcription	Primary B cells from cord blood	blood
39	chr5:96050800-96053000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:96050800-96053200	Weak transcription	Gastric	stomach
41	chr5:96050800-96053400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:96050800-96057200	Weak transcription	Ovary	ovary
43	chr5:96051000-96053000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr5:96051000-96053000	Enhancers	Primary T cells from cord blood	blood
45	chr5:96051000-96053200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:96051000-96053800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:96051000-96053800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr5:96051000-96054000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:96051000-96054400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:96051000-96054400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links