Variant report

Variant	rs4748572
Chromosome Location	chr10:5774915-5774916
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:5772758..5775590-chr10:5788161..5791817,4	K562	blood:
2	chr10:5732189..5734942-chr10:5774754..5777305,2	K562	blood:

Variant related genes	Relation type
ENSG00000108021	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1046393	1.00[CHD][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1129614	1.00[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11920	1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs1858446	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.85[YRI][hapmap];0.89[ASN][1000 genomes]
rs2275774	0.81[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs2797496	0.94[CEU][hapmap];1.00[TSI][hapmap]
rs2890364	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3793707	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45575338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4748307	0.81[AFR][1000 genomes]
rs4749379	0.94[CHB][hapmap];1.00[YRI][hapmap]
rs4750553	0.89[ASW][hapmap]
rs55837307	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55910451	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55913768	0.81[AFR][1000 genomes]
rs56033057	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56251728	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58859669	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59007376	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61832743	0.81[AFR][1000 genomes]
rs7095103	0.91[ASN][1000 genomes]
rs72772354	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72772355	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72772358	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72772376	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72772390	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72772400	0.85[ASN][1000 genomes]
rs72774056	0.81[AFR][1000 genomes]
rs72774070	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72774075	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72774077	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72774078	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74116316	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv1050663	chr10:5737979-5785918	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4748572	GDI2	cis	Artery Tibial	GTEx
rs4748572	GDI2	Cis_1M	lymphoblastoid	RTeQTL
rs4748572	GDI2	cis	cerebellum	SCAN
rs4748572	GDI2	cis	Whole Blood	GTEx
rs4748572	GDI2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5753800-5783400	Weak transcription	Brain Substantia Nigra	brain
2	chr10:5753800-5787000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr10:5754400-5781600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr10:5762200-5783000	Weak transcription	Stomach Mucosa	stomach
5	chr10:5762200-5795400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr10:5762400-5775000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr10:5762400-5794600	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr10:5762600-5843400	Strong transcription	Dnd41	blood
9	chr10:5762800-5775200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr10:5762800-5778000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr10:5762800-5778000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr10:5762800-5779800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr10:5762800-5793000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr10:5762800-5843000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:5763000-5795000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr10:5763200-5778800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr10:5763200-5779000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:5763400-5788600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr10:5763800-5775000	Strong transcription	Liver	Liver
20	chr10:5764200-5775600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr10:5765400-5775800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr10:5765600-5775000	Strong transcription	Placenta	Placenta
23	chr10:5765600-5775600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr10:5766600-5777400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr10:5767200-5792800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr10:5767600-5775000	Strong transcription	Adipose Nuclei	Adipose
27	chr10:5767600-5775800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr10:5768000-5788400	Weak transcription	Fetal Brain Male	brain
29	chr10:5768000-5849400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr10:5768200-5775600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr10:5768200-5775600	Strong transcription	Osteobl	bone
32	chr10:5768400-5775600	Strong transcription	Primary T cells from cord blood	blood
33	chr10:5768400-5775600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr10:5768400-5778000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr10:5768600-5786400	Strong transcription	GM12878-XiMat	blood
36	chr10:5768800-5775000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:5768800-5775000	Strong transcription	NH-A	brain
38	chr10:5768800-5777400	Strong transcription	Fetal Muscle Leg	muscle
39	chr10:5768800-5778200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr10:5769000-5775000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr10:5769000-5775000	Strong transcription	Thymus	Thymus
42	chr10:5769400-5784200	Weak transcription	Psoas Muscle	Psoas
43	chr10:5769600-5775000	Strong transcription	HSMM	muscle
44	chr10:5769600-5781600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr10:5769800-5775600	Strong transcription	Fetal Stomach	stomach
46	chr10:5770600-5776000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr10:5771200-5775000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr10:5771200-5775000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr10:5771200-5778600	Strong transcription	Fetal Intestine Large	intestine
50	chr10:5771400-5775000	Strong transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links