Variant report

Variant	rs4604177
Chromosome Location	chr5:74808880-74808881
allele	C/T
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	CUX1	chr5:74808851-74809126	K562	blood:	n/a	n/a
2	CBX3	chr5:74808454-74808929	K562	blood:	n/a	n/a
3	POLR2A	chr5:74807206-74808916	GM12891	blood:	n/a	n/a
4	SREBP1	chr5:74807187-74809330	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74808217..74810593-chr5:74816041..74817596,2	K562	blood:
2	chr5:74808667..74810597-chr5:74818060..74820048,3	K562	blood:

Variant related genes	Relation type
COL4A3BP	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10045497	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10474433	0.86[GIH][hapmap]
rs11748027	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11749783	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs12654264	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs12916	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2307111	0.89[ASW][hapmap]
rs253414	0.82[GIH][hapmap]
rs2878417	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs34358	0.81[GIH][hapmap]
rs3843480	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3843481	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3846662	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs3846663	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs40060	0.81[GIH][hapmap]
rs4549504	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4704219	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4704220	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4704221	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4704223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4704227	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5744552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5744672	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5744680	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5744696	0.85[YRI][hapmap]
rs6873472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6878990	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6896136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7703051	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs7703282	0.81[AMR][1000 genomes]
rs7733436	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs984976	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv882198	chr5:74736065-74896798	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv882200	chr5:74781439-74830808	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv882201	chr5:74787310-74890618	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
11	nsv882202	chr5:74808417-74946455	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4604177	TNPO1	cis	cerebellum	SCAN
rs4604177	HMGCR	cis	cerebellum	SCAN
rs4604177	HMGCR	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74804000-74809000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:74804600-74809800	Active TSS	NHLF	lung
3	chr5:74804800-74809600	Active TSS	K562	blood
4	chr5:74805000-74810200	Active TSS	GM12878-XiMat	blood
5	chr5:74805200-74809000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr5:74805200-74809000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:74805200-74809000	Active TSS	NHDF-Ad	bronchial
8	chr5:74805200-74809400	Active TSS	Right Atrium	heart
9	chr5:74805400-74809000	Active TSS	Ovary	ovary
10	chr5:74805400-74809200	Active TSS	HSMM	muscle
11	chr5:74805400-74809400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:74805800-74809000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr5:74806000-74809000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:74807200-74809600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:74807400-74809800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:74808000-74809200	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr5:74808000-74809800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:74808000-74809800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:74808000-74809800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr5:74808000-74814600	Weak transcription	Gastric	stomach
21	chr5:74808200-74809000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr5:74808200-74809200	Flanking Active TSS	Fetal Lung	lung
23	chr5:74808200-74809400	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr5:74808200-74809800	Flanking Active TSS	Dnd41	blood
25	chr5:74808200-74814600	Weak transcription	Left Ventricle	heart
26	chr5:74808200-74814600	Weak transcription	Pancreas	Pancrea
27	chr5:74808200-74814800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:74808200-74817600	Weak transcription	Esophagus	oesophagus
29	chr5:74808400-74809000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:74808400-74809000	Enhancers	Primary T cells fromperipheralblood	blood
31	chr5:74808400-74809000	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr5:74808400-74809000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr5:74808400-74809000	Enhancers	Small Intestine	intestine
34	chr5:74808400-74809000	Flanking Active TSS	Hela-S3	cervix
35	chr5:74808400-74809400	Enhancers	Primary T cells from cord blood	blood
36	chr5:74808400-74809400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr5:74808400-74809400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr5:74808400-74809400	Enhancers	Fetal Intestine Small	intestine
39	chr5:74808400-74809400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr5:74808400-74809400	Flanking Active TSS	Osteobl	bone
41	chr5:74808400-74809600	Enhancers	Primary hematopoietic stem cells	blood
42	chr5:74808400-74809600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr5:74808400-74809600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr5:74808400-74809600	Flanking Active TSS	NHEK	skin
45	chr5:74808400-74809800	Enhancers	Fetal Heart	heart
46	chr5:74808400-74810000	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr5:74808400-74810000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr5:74808400-74812000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:74808400-74812000	Enhancers	Primary B cells from cord blood	blood
50	chr5:74808400-74812400	Enhancers	Primary B cells from peripheral blood	blood

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