Variant report

Variant	rs3793707
Chromosome Location	chr10:5798730-5798731
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:5798637-5798933	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr10:5798429-5801163	GM12878	blood:	n/a	n/a
3	POLR2A	chr10:5798629-5810250	K562	blood:	n/a	n/a
4	POLR2A	chr10:5798571-5803731	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:5795768..5800439-chr10:5800634..5804425,4	K562	blood:
2	chr10:5795316..5797581-chr10:5797846..5800735,2	MCF-7	breast:

Variant related genes	Relation type
FAM208B	TF binding region
ENSG00000108021	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1046393	1.00[CHD][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1129614	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11920	1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs1858446	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2275774	0.87[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs2797496	0.82[CEU][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs2890364	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs45575338	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4748572	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]
rs4749379	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap]
rs4750553	0.89[ASW][hapmap]
rs55837307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55910451	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56033057	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56251728	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58859669	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59007376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7095103	0.88[ASN][1000 genomes]
rs72772354	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72772355	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72772358	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72772376	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72772390	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72772400	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72774070	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72774075	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72774077	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72774078	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74116316	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[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	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3793707	GDI2	cis	parietal	SCAN
rs3793707	GDI2	cis	cerebellum	SCAN
rs3793707	GDI2	Cis_1M	lymphoblastoid	RTeQTL
rs3793707	GDI2	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5762600-5843400	Strong transcription	Dnd41	blood
2	chr10:5762800-5843000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:5768000-5849400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:5779000-5804600	Strong transcription	A549	lung
5	chr10:5781400-5818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr10:5783400-5816600	Strong transcription	Primary B cells from peripheral blood	blood
7	chr10:5784800-5799400	Weak transcription	Colon Smooth Muscle	Colon
8	chr10:5784800-5818000	Weak transcription	Stomach Mucosa	stomach
9	chr10:5786200-5816400	Weak transcription	Right Atrium	heart
10	chr10:5788000-5818000	Strong transcription	Duodenum Mucosa	Duodenum
11	chr10:5789200-5799000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr10:5789200-5804400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr10:5790400-5798800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr10:5790600-5800200	Weak transcription	Fetal Brain Male	brain
15	chr10:5790800-5799000	Weak transcription	HSMMtube	muscle
16	chr10:5790800-5799200	Weak transcription	HUVEC	blood vessel
17	chr10:5791200-5799200	Weak transcription	Small Intestine	intestine
18	chr10:5791400-5798800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr10:5791800-5799000	Weak transcription	NHEK	skin
20	chr10:5792000-5799000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr10:5792000-5799200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr10:5792000-5799400	Weak transcription	Fetal Heart	heart
23	chr10:5792600-5798800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr10:5793800-5799600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr10:5794000-5798800	Weak transcription	Brain Hippocampus Middle	brain
26	chr10:5794000-5802600	Strong transcription	Fetal Stomach	stomach
27	chr10:5794600-5799000	Weak transcription	Right Ventricle	heart
28	chr10:5794600-5806600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr10:5794800-5799000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr10:5794800-5799000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr10:5794800-5799000	Weak transcription	Aorta	Aorta
32	chr10:5794800-5799000	Weak transcription	Gastric	stomach
33	chr10:5794800-5799000	Weak transcription	Pancreas	Pancrea
34	chr10:5794800-5799000	Weak transcription	Spleen	Spleen
35	chr10:5794800-5799200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr10:5795000-5798800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr10:5795000-5798800	Weak transcription	GM12878-XiMat	blood
38	chr10:5795000-5799000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr10:5795000-5800400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr10:5795000-5800600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr10:5795000-5817800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr10:5795200-5799000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr10:5795200-5804200	Strong transcription	Fetal Intestine Small	intestine
44	chr10:5795400-5798800	Weak transcription	NHDF-Ad	bronchial
45	chr10:5795400-5799000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr10:5795800-5799000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr10:5795800-5799000	Weak transcription	Esophagus	oesophagus
48	chr10:5796000-5799000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr10:5796000-5822400	Strong transcription	Fetal Intestine Large	intestine
50	chr10:5796400-5799000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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