Variant report

Variant	rs9131
Chromosome Location	chr4:74963049-74963050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:74913574..74916451-chr4:74961099..74963523,2	K562	blood:
2	chr4:74962104..74964124-chr4:75017131..75019515,2	K562	blood:
3	chr4:74962349..74965298-chr4:74989325..74991389,2	K562	blood:
4	chr4:74925941..74928712-chr4:74962459..74964831,3	K562	blood:
5	chr4:74917692..74925936-chr4:74958187..74967502,26	K562	blood:
6	chr4:74918446..74926481-chr4:74958079..74968779,32	K562	blood:
7	chr4:74933317..74934864-chr4:74961700..74963959,2	K562	blood:

Variant related genes	Relation type
ENSG00000163738	Chromatin interaction
ENSG00000248848	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10938107	0.83[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs11725704	0.89[EUR][1000 genomes]
rs11733208	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs12642974	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs13124617	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13128896	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1371794	0.89[EUR][1000 genomes]
rs1371798	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1371799	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1837559	0.91[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs1866755	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806792	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4121652	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs518867	0.89[EUR][1000 genomes]
rs546829	0.86[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs549280	0.86[EUR][1000 genomes]
rs72652928	0.88[EUR][1000 genomes]
rs72652934	0.85[EUR][1000 genomes]
rs7667376	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684973	0.91[JPT][hapmap];0.81[AMR][1000 genomes]
rs7686861	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs882638	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs981458	0.83[EUR][1000 genomes]

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	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1006029	chr4:74793922-74986664	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv3443825	chr4:74903785-74964443	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9131	CXCL6	cis	parietal	SCAN
rs9131	UTP3	cis	parietal	SCAN
rs9131	G3BP2	cis	parietal	SCAN
rs9131	CCNG2	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74954800-74963800	Weak transcription	HSMMtube	muscle
2	chr4:74958400-74963400	Enhancers	Fetal Intestine Large	intestine
3	chr4:74958800-74964200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:74959000-74963800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:74959400-74963400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:74959400-74963400	Weak transcription	Stomach Mucosa	stomach
7	chr4:74959400-74963400	Weak transcription	NHEK	skin
8	chr4:74959800-74963200	Weak transcription	Pancreas	Pancrea
9	chr4:74959800-74963400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:74960000-74963400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:74960000-74963400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:74960200-74963200	Weak transcription	Lung	lung
13	chr4:74960200-74963400	Weak transcription	Gastric	stomach
14	chr4:74960200-74964400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:74960400-74963400	Weak transcription	Spleen	Spleen
16	chr4:74960400-74963400	Weak transcription	Dnd41	blood
17	chr4:74960400-74963600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr4:74960400-74963600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:74960800-74963400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr4:74961000-74963400	Enhancers	Fetal Intestine Small	intestine
21	chr4:74961200-74963400	Active TSS	Liver	Liver
22	chr4:74961200-74965200	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr4:74961600-74963400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr4:74961600-74963600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:74962000-74963400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:74962200-74963400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:74962400-74964200	Transcr. at gene 5' and 3'	K562	blood
28	chr4:74962400-74965000	Active TSS	Adipose Nuclei	Adipose
29	chr4:74962600-74964800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:74962800-74963200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:74962800-74963200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr4:74962800-74965400	Active TSS	A549	lung
33	chr4:74962800-74965600	Active TSS	Right Atrium	heart
34	chr4:74963000-74963200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:74963000-74963200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr4:74963000-74963200	Flanking Active TSS	HUVEC	blood vessel
37	chr4:74963000-74963400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:74963000-74963400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:74963000-74963400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:74963000-74963400	Active TSS	Hela-S3	cervix
41	chr4:74963000-74963400	Active TSS	HMEC	breast
42	chr4:74963000-74963400	Active TSS	Monocytes-CD14+_RO01746	blood
43	chr4:74963000-74963600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:74963000-74964600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr4:74963000-74964600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:74963000-74965400	Active TSS	Left Ventricle	heart
47	chr4:74963000-74965600	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr4:74963000-74965600	Active TSS	Psoas Muscle	Psoas

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