Variant report

Variant	rs7655464
Chromosome Location	chr4:76676277-76676278
allele	A/G
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	SETDB1	chr4:76676118-76676318	U2OS	brain:	n/a	n/a
2	POLR2A	chr4:76676109-76676283	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76670707..76672414-chr4:76675811..76678337,2	K562	blood:

Variant related genes	Relation type
USO1	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10016782	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10028291	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10031616	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10033315	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10212995	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097112	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097113	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097122	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11728073	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730896	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11932454	0.81[EUR][1000 genomes]
rs11938067	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11943497	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12505149	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13102733	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13110602	0.91[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133144	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13133472	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13134891	0.88[AMR][1000 genomes]
rs13145290	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13147276	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2047989	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2055997	0.86[JPT][hapmap]
rs2271472	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2869175	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2904018	0.84[ASN][1000 genomes]
rs3796479	0.81[CHD][hapmap]
rs3796481	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4446339	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859404	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859405	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4859406	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859408	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859409	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859549	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859552	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859554	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859555	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55664143	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62318556	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6531901	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6829993	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6843016	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6845147	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6846575	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6847333	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7661037	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7665517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs905954	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs987561	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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	51 gene(s)	inside rSNPs	diseases
2	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
3	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7655464	USO1	cis	cerebellum	SCAN
rs7655464	CDKL2	cis	parietal	SCAN
rs7655464	CXCL10	cis	parietal	SCAN
rs7655464	CCNG2	cis	cerebellum	SCAN
rs7655464	SCARB2	cis	parietal	SCAN
rs7655464	PAQR3	cis	cerebellum	SCAN
rs7655464	FAM47E	cis	parietal	SCAN
rs7655464	PPEF2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76650800-76737800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:76652000-76696400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:76652400-76725000	Weak transcription	Hela-S3	cervix
4	chr4:76659800-76679000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:76668400-76698600	Weak transcription	Fetal Brain Male	brain
6	chr4:76671000-76689400	Weak transcription	Fetal Heart	heart
7	chr4:76671000-76739400	Weak transcription	Stomach Mucosa	stomach
8	chr4:76671600-76707800	Weak transcription	Right Ventricle	heart
9	chr4:76672000-76692200	Weak transcription	Colonic Mucosa	Colon
10	chr4:76673200-76677400	Strong transcription	Fetal Muscle Leg	muscle
11	chr4:76673400-76676800	Strong transcription	Fetal Intestine Large	intestine
12	chr4:76673400-76677000	Strong transcription	Osteobl	bone
13	chr4:76673600-76677000	Strong transcription	Fetal Muscle Trunk	muscle
14	chr4:76673600-76680200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:76674600-76676400	Strong transcription	Lung	lung
16	chr4:76674600-76677200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr4:76674600-76678000	Strong transcription	Fetal Stomach	stomach
18	chr4:76674600-76679800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:76674800-76715200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:76675000-76676800	Strong transcription	Small Intestine	intestine
21	chr4:76675000-76727400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:76675200-76676400	Strong transcription	Pancreas	Pancrea
23	chr4:76675200-76676600	Strong transcription	Fetal Kidney	kidney
24	chr4:76675200-76676800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:76675200-76676800	Strong transcription	Ovary	ovary
26	chr4:76675200-76676800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:76675200-76677000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr4:76675200-76677000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:76675200-76677000	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:76675200-76677200	Strong transcription	Duodenum Mucosa	Duodenum
31	chr4:76675200-76677200	Strong transcription	Fetal Thymus	thymus
32	chr4:76675200-76677600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:76675200-76677600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:76675200-76677600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:76675200-76677600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:76675200-76677800	Strong transcription	Adipose Nuclei	Adipose
37	chr4:76675200-76678000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:76675200-76678800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:76675200-76680000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:76675200-76681200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:76675400-76676800	Strong transcription	Primary T cells from cord blood	blood
42	chr4:76675400-76676800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr4:76675400-76676800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr4:76675400-76676800	Strong transcription	HMEC	breast
45	chr4:76675400-76677000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr4:76675400-76677000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr4:76675400-76677000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:76675400-76677000	Strong transcription	Left Ventricle	heart
49	chr4:76675400-76677200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:76675400-76677200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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