Variant report

Variant	rs904451
Chromosome Location	chr4:186630946-186630947
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10016122	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10017672	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs10017940	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs10019263	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs1003004	0.80[ASN][1000 genomes]
rs11132336	0.83[ASN][1000 genomes]
rs11132337	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11132339	0.85[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap]
rs11725010	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11733264	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11932587	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11937510	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11941721	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12640689	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12643220	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12649216	0.80[ASN][1000 genomes]
rs13119888	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs1566349	0.90[EUR][1000 genomes]
rs1566351	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1566352	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1566353	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2030143	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2047499	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs4862565	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs6812761	0.83[ASN][1000 genomes]
rs6820044	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs6825114	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs6825669	0.84[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap]
rs6826210	0.85[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap]
rs6836237	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs6837079	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs7673413	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7689859	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7690098	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7695346	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9991426	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9991548	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432684	chr4:186412851-186742851	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv830169	chr4:186455064-186638163	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1028146	chr4:186503899-187338335	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1020731	chr4:186512433-186724031	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1023917	chr4:186533075-186997806	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv537420	chr4:186533075-186997806	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv830171	chr4:186610113-186789271	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1023412	chr4:186613289-186707428	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv537421	chr4:186613289-186707428	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv427702	chr4:186618031-186782377	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs904451	PDLIM3	cis	cerebellum	SCAN
rs904451	STK40	trans	brain	seeQTL
rs904451	PPTC7	trans	brain	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:186622000-186651800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:186622600-186637200	Weak transcription	Colon Smooth Muscle	Colon
3	chr4:186623600-186633600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:186625600-186633000	Weak transcription	Ovary	ovary
5	chr4:186626200-186631800	Weak transcription	Esophagus	oesophagus
6	chr4:186626400-186632200	Weak transcription	Aorta	Aorta
7	chr4:186626400-186633000	Weak transcription	Gastric	stomach
8	chr4:186626400-186633600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:186627000-186633000	Weak transcription	Fetal Stomach	stomach
10	chr4:186627200-186633000	Weak transcription	Pancreas	Pancrea
11	chr4:186627200-186639800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:186627800-186633600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:186627800-186633800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:186628200-186637600	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr4:186628400-186631600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:186628600-186632200	Enhancers	NHDF-Ad	bronchial
17	chr4:186628600-186632800	Enhancers	Rectal Smooth Muscle	rectum
18	chr4:186629000-186635400	Enhancers	HUVEC	blood vessel
19	chr4:186629200-186633600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr4:186629200-186634400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:186629400-186632800	Weak transcription	Fetal Intestine Large	intestine
22	chr4:186629400-186633400	Weak transcription	Small Intestine	intestine
23	chr4:186629600-186632600	Enhancers	Fetal Heart	heart
24	chr4:186629600-186632800	Weak transcription	Fetal Intestine Small	intestine
25	chr4:186629600-186633400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:186629600-186634200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:186629800-186633400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:186630000-186631600	Enhancers	Osteobl	bone
29	chr4:186630000-186631800	Weak transcription	Right Ventricle	heart
30	chr4:186630000-186633200	Weak transcription	Left Ventricle	heart
31	chr4:186630000-186651600	Weak transcription	HSMM	muscle
32	chr4:186630600-186632200	Enhancers	Hela-S3	cervix
33	chr4:186630600-186633400	Enhancers	HepG2	liver
34	chr4:186630600-186634600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr4:186630600-186635200	Enhancers	HMEC	breast
36	chr4:186630600-186635200	Enhancers	NH-A	brain
37	chr4:186630800-186631000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:186630800-186631000	Enhancers	Lung	lung
39	chr4:186630800-186631200	Genic enhancers	HSMMtube	muscle
40	chr4:186630800-186632000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:186630800-186632600	Enhancers	Right Atrium	heart
42	chr4:186630800-186632600	Weak transcription	Stomach Mucosa	stomach
43	chr4:186630800-186632800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:186630800-186632800	Enhancers	Liver	Liver

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