Variant report

Variant	rs10057864
Chromosome Location	chr5:102884838-102884839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:149223276..149223928-chr5:102884822..102885391,2	MCF-7	breast:
2	chr5:102882600..102886619-chr5:102891245..102894545,3	K562	blood:
3	chr5:102880417..102882081-chr5:102883836..102886115,2	K562	blood:

Variant related genes	Relation type
ENSG00000112874	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10061242	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078744	1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13157247	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13356231	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28406419	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34672333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35355522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878912	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880267	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71586376	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73190066	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7707836	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716935	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7723689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725090	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7730302	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734923	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9327885	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882523	chr5:102687151-103342745	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1031600	chr5:102728430-103013575	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1025561	chr5:102744280-103152495	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv537832	chr5:102744280-103152495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1025859	chr5:102744479-103710290	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv537833	chr5:102744479-103710290	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10057864	NUDT12	cis	Skin Sun Exposed Lower leg	GTEx
rs10057864	NUDT12	Cis_1M	lymphoblastoid	RTeQTL
rs10057864	RAB9BP1	cis	parietal	SCAN
rs10057864	NUDT12	cis	parietal	SCAN
rs10057864	ST8SIA4	cis	parietal	SCAN
rs10057864	NUDT12	cis	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:102874200-102897400	Weak transcription	Pancreas	Pancrea
2	chr5:102875400-102887800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:102875800-102897800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:102876600-102886000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:102876800-102887800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:102877000-102886000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:102877200-102888000	Weak transcription	Stomach Mucosa	stomach
8	chr5:102878400-102887800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:102878600-102885800	Weak transcription	Osteobl	bone
10	chr5:102878800-102886400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:102879800-102897200	Weak transcription	Brain Germinal Matrix	brain
12	chr5:102879800-102897400	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:102880000-102885400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:102880200-102886600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:102880200-102886800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:102880200-102897200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:102880800-102886600	Weak transcription	Left Ventricle	heart
18	chr5:102881000-102885400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:102881200-102897800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:102882200-102886800	Weak transcription	HSMM	muscle
21	chr5:102882400-102897400	Weak transcription	Psoas Muscle	Psoas
22	chr5:102882800-102897400	Weak transcription	Fetal Heart	heart
23	chr5:102882800-102897600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:102883000-102889200	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:102883200-102897400	Weak transcription	GM12878-XiMat	blood
26	chr5:102883600-102885400	Weak transcription	Liver	Liver
27	chr5:102883800-102885400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:102883800-102885600	Weak transcription	Adipose Nuclei	Adipose
29	chr5:102884000-102885600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:102884000-102885600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:102884000-102885600	Weak transcription	HMEC	breast
32	chr5:102884000-102886600	Weak transcription	Fetal Lung	lung
33	chr5:102884000-102891600	Weak transcription	Gastric	stomach
34	chr5:102884200-102885800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr5:102884200-102885800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:102884200-102885800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr5:102884200-102885800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr5:102884200-102886000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:102884200-102886000	Weak transcription	Fetal Kidney	kidney
40	chr5:102884200-102889200	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr5:102884200-102894000	Weak transcription	NHEK	skin
42	chr5:102884400-102886000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr5:102884400-102886200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:102884400-102886600	Weak transcription	Brain Anterior Caudate	brain
45	chr5:102884600-102886200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:102884600-102886400	Weak transcription	Fetal Intestine Large	intestine
47	chr5:102884600-102897400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr5:102884600-102897400	Weak transcription	HSMMtube	muscle
49	chr5:102884600-102897400	Weak transcription	NH-A	brain
50	chr5:102884600-102898000	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links