Variant report

Variant	rs10507177
Chromosome Location	chr12:105008908-105008909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104995437..104998034-chr12:105002964..105009191,6	K562	blood:
2	chr12:104995437..104998034-chr12:105005195..105009191,4	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10778343	0.89[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs10778346	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10861255	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10861256	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11112132	0.98[ASN][1000 genomes]
rs11112136	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541795	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1896563	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964826	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7133744	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7304590	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs875679	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[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	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1050695	chr12:105000981-105125161	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv541589	chr12:105000981-105125161	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10507177	UTP20	cis	parietal	SCAN
rs10507177	NLRP4	trans	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104989400-105030600	Strong transcription	Dnd41	blood
2	chr12:104993200-105012600	Weak transcription	Gastric	stomach
3	chr12:104998600-105012800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:104998800-105031400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:104999000-105026800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:104999800-105012800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:105000000-105020400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:105000000-105021000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:105000400-105009200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:105000400-105014600	Weak transcription	Osteobl	bone
11	chr12:105000400-105014800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:105000400-105019800	Weak transcription	HMEC	breast
13	chr12:105000400-105026000	Weak transcription	NHLF	lung
14	chr12:105000600-105012800	Weak transcription	Lung	lung
15	chr12:105002800-105013800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:105003200-105014200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:105003600-105014600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:105003600-105020200	Weak transcription	NHEK	skin
19	chr12:105004600-105015000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr12:105004800-105013200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:105005800-105019800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:105006000-105012400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr12:105006000-105014800	Weak transcription	Spleen	Spleen
24	chr12:105006000-105016400	Weak transcription	A549	lung
25	chr12:105006000-105028200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:105006200-105012600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr12:105006200-105012800	Weak transcription	Fetal Thymus	thymus
28	chr12:105006200-105034800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:105006400-105014000	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:105006600-105012400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:105006600-105022600	Weak transcription	Primary B cells from cord blood	blood
32	chr12:105006800-105009400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:105007000-105010600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:105007000-105012600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr12:105007200-105012600	Weak transcription	GM12878-XiMat	blood
36	chr12:105007400-105010000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:105007400-105012400	Weak transcription	K562	blood
38	chr12:105007400-105024400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr12:105007600-105012600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:105007800-105009000	Strong transcription	Thymus	Thymus
41	chr12:105007800-105012600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr12:105007800-105015600	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr12:105008000-105009400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:105008000-105010000	Enhancers	Fetal Brain Female	brain
45	chr12:105008000-105011000	Enhancers	Fetal Stomach	stomach
46	chr12:105008200-105009400	Enhancers	Placenta	Placenta
47	chr12:105008400-105009000	Enhancers	Esophagus	oesophagus
48	chr12:105008400-105009200	Enhancers	Aorta	Aorta
49	chr12:105008400-105009200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr12:105008400-105009200	Flanking Active TSS	Stomach Smooth Muscle	stomach

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