Variant report

Variant	rs10057868
Chromosome Location	chr5:178992685-178992686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178992676..178996882-chr5:179050015..179052234,4	K562	blood:
2	chr5:178991096..178994000-chr5:178994365..178996408,2	K562	blood:
3	chr5:178984205..178987569-chr5:178988108..178992792,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169045	Chromatin interaction
ENSG00000176783	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10036118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056863	0.80[JPT][hapmap]
rs10059134	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064557	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11249645	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249646	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11743261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521172	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522890	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12719865	0.80[JPT][hapmap];0.80[YRI][hapmap]
rs13361148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28510162	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28607444	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28611242	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075890	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075891	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700810	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4701134	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4701140	0.80[CHD][hapmap]
rs6601052	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6895677	0.80[JPT][hapmap]
rs7378831	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7447429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7706275	0.80[JPT][hapmap];0.85[YRI][hapmap]
rs9329083	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9329084	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	esv2758031	chr5:178661266-179037529	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv2759397	chr5:178661266-179037529	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv2829850	chr5:178828854-179060995	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
5	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
6	nsv1022509	chr5:178950829-179002751	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv883269	chr5:178951106-179031595	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
9	nsv1015477	chr5:178954409-179016804	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv883271	chr5:178955046-179031595	Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv883272	chr5:178961872-179031595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv1028236	chr5:178962087-179019981	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10057868	RUFY1	cis	cerebellum	SCAN
rs10057868	RNF44	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178981200-178996200	Weak transcription	K562	blood
2	chr5:178986400-179000400	Strong transcription	Dnd41	blood
3	chr5:178987200-178995800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:178987200-179040800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:178987400-178993800	Weak transcription	Esophagus	oesophagus
6	chr5:178987400-178995600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:178987400-178995800	Weak transcription	Fetal Heart	heart
8	chr5:178987400-178996000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:178987400-178996000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:178987400-178996200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:178987400-178997400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:178987400-179000000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr5:178987400-179000200	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr5:178987400-179013200	Strong transcription	Fetal Stomach	stomach
15	chr5:178987400-179019800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:178987600-179045600	Strong transcription	Fetal Intestine Small	intestine
17	chr5:178987800-178995000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:178987800-178995200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:178987800-178995800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr5:178987800-178999800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:178987800-179000000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:178987800-179006600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:178987800-179006800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:178987800-179009600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr5:178987800-179012200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:178987800-179017000	Strong transcription	Osteobl	bone
27	chr5:178987800-179031000	Strong transcription	Fetal Muscle Leg	muscle
28	chr5:178987800-179045600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:178988000-178995000	Strong transcription	Brain Hippocampus Middle	brain
30	chr5:178988000-178995600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:178988000-179000200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr5:178988000-179000400	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr5:178988000-179000400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:178988000-179004600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:178988000-179006800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:178988000-179009600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:178988200-178997400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:178988200-178999200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:178988200-178999200	Strong transcription	Liver	Liver
40	chr5:178988200-178999800	Strong transcription	Fetal Intestine Large	intestine
41	chr5:178988200-179000400	Strong transcription	HepG2	liver
42	chr5:178988200-179003400	Strong transcription	Placenta	Placenta
43	chr5:178988400-178995600	Strong transcription	Adipose Nuclei	Adipose
44	chr5:178988400-179000000	Strong transcription	Rectal Smooth Muscle	rectum
45	chr5:178988400-179002800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:178988400-179006200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr5:178988400-179006600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr5:178988400-179010200	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr5:178988600-178999800	Strong transcription	Brain Anterior Caudate	brain
50	chr5:178988800-179003200	Strong transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links