Variant report

Variant	rs10778343
Chromosome Location	chr12:105003006-105003007
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104997510..104999903-chr12:105002089..105003876,3	MCF-7	breast:
2	chr12:104995437..104998034-chr12:105002964..105009191,6	K562	blood:
3	chr12:104995476..104999568-chr12:105000294..105003603,4	MCF-7	breast:
4	chr12:104996399..104998456-chr12:105002964..105004800,2	K562	blood:
5	chr12:105001524..105004120-chr12:105024508..105026031,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10507177	0.89[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs10861255	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11112136	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs1541795	0.84[EUR][1000 genomes]
rs1896563	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs68011462	0.81[ASN][1000 genomes]
rs875679	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1035364	chr12:104948307-105003705	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
rs10778343	NLRP4	trans	cerebellum	SCAN
rs10778343	UTP20	cis	parietal	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	chr12:104993200-105006200	Weak transcription	Fetal Heart	heart
3	chr12:104993200-105012600	Weak transcription	Gastric	stomach
4	chr12:104997200-105003800	Weak transcription	Fetal Brain Male	brain
5	chr12:104997200-105004600	Enhancers	Placenta	Placenta
6	chr12:104998000-105004400	Weak transcription	Stomach Mucosa	stomach
7	chr12:104998000-105008600	Weak transcription	Right Ventricle	heart
8	chr12:104998200-105003200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:104998200-105008400	Weak transcription	Esophagus	oesophagus
10	chr12:104998400-105003400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:104998400-105005000	Weak transcription	Spleen	Spleen
12	chr12:104998400-105008400	Weak transcription	Aorta	Aorta
13	chr12:104998400-105008400	Weak transcription	Right Atrium	heart
14	chr12:104998400-105008600	Weak transcription	Small Intestine	intestine
15	chr12:104998600-105003200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr12:104998600-105003200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:104998600-105003800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:104998600-105005200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:104998600-105008600	Weak transcription	Primary T cells from cord blood	blood
20	chr12:104998600-105012800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:104998800-105031400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:104999000-105005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr12:104999000-105026800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:104999600-105003600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:104999600-105004000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr12:104999800-105004200	Weak transcription	GM12878-XiMat	blood
27	chr12:104999800-105005200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:104999800-105005400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr12:104999800-105005600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:104999800-105008800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:104999800-105012800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:105000000-105004600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr12:105000000-105005400	Weak transcription	Primary B cells from cord blood	blood
34	chr12:105000000-105020400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:105000000-105021000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:105000200-105004800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:105000200-105008400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:105000400-105004000	Weak transcription	A549	lung
39	chr12:105000400-105008400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:105000400-105008400	Weak transcription	Adipose Nuclei	Adipose
41	chr12:105000400-105009200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:105000400-105014600	Weak transcription	Osteobl	bone
43	chr12:105000400-105014800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:105000400-105019800	Weak transcription	HMEC	breast
45	chr12:105000400-105026000	Weak transcription	NHLF	lung
46	chr12:105000600-105005800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:105000600-105012800	Weak transcription	Lung	lung
48	chr12:105000800-105008600	Weak transcription	HSMMtube	muscle
49	chr12:105001000-105006600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr12:105001400-105006200	Strong transcription	Fetal Thymus	thymus

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